From 5f45117575446a96d310d14f8881fe02370694dd Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Wed, 29 Nov 2017 19:17:09 +0200
Subject: [PATCH 01/31] API-106 #comment Initial implementation of a vcf
 annotator class. Wrapper classes for json to python objects to improve access
 of annotation results

---
 annotate_vcf.py                               |  39 +++
 setup.py                                      |   4 +-
 simpleVCFClient.py                            | 229 ------------------
 variantapi/models/__init__.py                 |   3 +
 variantapi/models/elements/__init__.py        |  17 ++
 variantapi/models/elements/broad.py           |  64 +++++
 variantapi/models/elements/dann.py            |   8 +
 variantapi/models/elements/dbnsfp.py          | 110 +++++++++
 variantapi/models/elements/gerp.py            |   9 +
 variantapi/models/elements/gnomad.py          |  64 +++++
 variantapi/models/elements/gwas.py            |  28 +++
 variantapi/models/elements/iarc.py            |  41 ++++
 variantapi/models/elements/icgc.py            |  18 ++
 variantapi/models/elements/isb.py             |  10 +
 variantapi/models/elements/ncbi.py            |  44 ++++
 variantapi/models/elements/sanger.py          |  82 +++++++
 .../models/elements/thousand_genomes.py       |  21 ++
 variantapi/models/elements/transcript.py      |  22 ++
 variantapi/models/elements/uniprot.py         |  21 ++
 variantapi/models/elements/wustl.py           |  32 +++
 variantapi/models/fields.py                   |   9 +
 variantapi/models/variant.py                  |  47 ++++
 variantapi/vcf.py                             |  52 ++++
 23 files changed, 744 insertions(+), 230 deletions(-)
 create mode 100755 annotate_vcf.py
 delete mode 100644 simpleVCFClient.py
 create mode 100644 variantapi/models/__init__.py
 create mode 100644 variantapi/models/elements/__init__.py
 create mode 100644 variantapi/models/elements/broad.py
 create mode 100644 variantapi/models/elements/dann.py
 create mode 100644 variantapi/models/elements/dbnsfp.py
 create mode 100644 variantapi/models/elements/gerp.py
 create mode 100644 variantapi/models/elements/gnomad.py
 create mode 100644 variantapi/models/elements/gwas.py
 create mode 100644 variantapi/models/elements/iarc.py
 create mode 100644 variantapi/models/elements/icgc.py
 create mode 100644 variantapi/models/elements/isb.py
 create mode 100644 variantapi/models/elements/ncbi.py
 create mode 100644 variantapi/models/elements/sanger.py
 create mode 100644 variantapi/models/elements/thousand_genomes.py
 create mode 100644 variantapi/models/elements/transcript.py
 create mode 100644 variantapi/models/elements/uniprot.py
 create mode 100644 variantapi/models/elements/wustl.py
 create mode 100644 variantapi/models/fields.py
 create mode 100644 variantapi/models/variant.py
 create mode 100644 variantapi/vcf.py

diff --git a/annotate_vcf.py b/annotate_vcf.py
new file mode 100755
index 0000000..b986173
--- /dev/null
+++ b/annotate_vcf.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+import argparse
+import json
+import logging
+import sys
+
+from variantapi.client import VariantAPIClient
+from variantapi.vcf import VCFAnnotator
+
+__author__ = 'ckopanos'
+logging.basicConfig(level=logging.DEBUG,
+                    format='[%(levelname)s]	%(threadName)s	%(message)s',
+                    )
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description='VCF Annotator command line')
+    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True)
+    parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
+                        required=False, default='hg19')
+    parser.add_argument('-f',
+                        help='Path to vcf file',
+                        type=str, metavar='VCF File', required=True)
+    parser.add_argument('-p',
+                        help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
+                        type=str, metavar='Request Params', required=False, nargs='+')
+    args = parser.parse_args()
+    api_key = args.k
+    vcf_file = args.f
+    ref_genome = args.g
+    request_parameters = None
+    if args.p:
+        request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
+    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parametes=request_parameters)
+    vcf_annotator.annotate(vcf_file)
+
+
+if __name__ == "__main__":
+    main(sys.argv[1:])
diff --git a/setup.py b/setup.py
index 5221bd9..18f99ff 100644
--- a/setup.py
+++ b/setup.py
@@ -29,6 +29,8 @@
         'Programming Language :: Python :: 3.5',
     ],
     install_requires=[
-        'requests>=2.0.0, <3.0.0'
+        'requests>=2.0.0, <3.0.0',
+        'PyVCF>=0.6.8',
+        'jsonmodels>=2.2'
     ],
 )
diff --git a/simpleVCFClient.py b/simpleVCFClient.py
deleted file mode 100644
index 6e6408d..0000000
--- a/simpleVCFClient.py
+++ /dev/null
@@ -1,229 +0,0 @@
-#!/usr/bin/env python3
-
-# A simple client application that does the following:
-# - Loads a VCF file,
-# - For each entry in the file, performs a lookup to the Saphetor Variant API. 
-#   The call can be either in batch mode (the default and more efficient way, 
-#   sending a number of variants at a time), or one by one. 
-# - Extends the VCF description to include gene information for each entry that
-#   is retreived from the response received from the API.
-# - Saves the result, including the gene information (a comma-separated list of 
-#   gene symbols for each variant) in a new file in the VCF format.
-#   Note that if a row in the input VCF file contains more than one ALT field 
-#   entries, i.e. corresponds to more than one variants, we'll be storing one
-#   row per variant in the output VCF file.
-#
-# It uses the following modules:
-# pyVCF (http://pyvcf.readthedocs.io/en/latest/) 
-# variantapi.client (https://github.com/saphetor/variant-api-client-python)
-
-import argparse
-import json
-import logging
-import vcf
-import re
-import sys
-from sys import argv
-from variantapi.client import VariantAPIClient
-from vcf.parser import _Info as VcfInfo, field_counts as vcf_field_counts
-
-__author__ = 'stephanos-androutsellis'
-
-# Declare reference genome as a global variable
-_ref_genome = 1019
-
-# Declare the limit of variants we want to lookup in each batch request
-_batch_limit = 3 
-
-
-# A class to store variant lookup data:
-# - The record from the input VCF file
-# - The variant string
-# - The corresponding ALT value (convenient for multi-variant records)
-class Variant_lookup_data(object):
-    vcf_record = None
-    variant_string = ""
-    alt_value = ""
-
-    # The class constructor/initializer 
-    def __init__(self,vcf_record,variant_string,alt_value):
-        self.vcf_record=vcf_record
-        self.variant_string=variant_string
-        self.alt_value=alt_value
-
-
-def main(argv):
-	# Read and parse arguments
-	infile = ''
-	outfile = ''
-	do_batch_lookups = True
-	input_error = False
-
-	parser = argparse.ArgumentParser(description='Simple VCF Client application')
-	parser.add_argument('-i', help='Input VCF file', type=str, metavar='Input File', required=True)
-	parser.add_argument('-o', help='Output VCF file', type=str, metavar='Output File', required=True)
-	parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
-	parser.add_argument('-g', help='Reference genome either 1019 (default) or 1038', type=int, 
-		metavar='Reference Genome', required=False, default=1019)
-	parser.add_argument('-nb', help="Do not do batch requests", action='store_true')
-
-	args = parser.parse_args()
-	infile = args.i
-	outfile = args.o
-	api_key = args.k
-	ref_genome = args.g if args.g is not None else _ref_genome
-	do_batch_lookups = not args.nb
-
-	# Open and load vcf file into vfc reader object
-	print ("Reading input file ", infile)
-	vcf_reader = vcf.Reader(filename=infile, encoding='utf8')
-
-	# Add a new GENE info field in the metadata description, so that we may store such data for each record
-	vcf_reader.infos['GENE'] = VcfInfo( 'GENE', ".", 'String', 'Concatenated list of GENE sumbols',"","")
-	
-	# Prepare output for writing.
-	print ("Opening output file ", outfile)
-	vcf_writer = vcf.Writer(open(outfile, 'w'), vcf_reader, lineterminator='\n')
-
-	# Declare an array of Variant_lookup_data objects to hold data for executing the
-	# lookups and process its outcome.
-	variant_lookup_data_array = []
-
-	# A counter for the total number of rows processed thus far
-	total_counter = 0
-
-	# Initialize client connection to API
-	api = VariantAPIClient(api_key)
-	if (api is None):
-		print("Failed to connect to API")
-		sys.exit()
-
-	print("Start parsing input file")
-
-	# Iterate throught all the records read from the input VCF file
-	while True:
-		try: 
-			# Get next record (corresponds to a data row in the file)
-			vcf_record = next(vcf_reader)
-
-			# A vcf_record (i.e. row in the VCF file) may correspond to more than one variants, if it contains 
-			# more than one ALT values. We generate a Variant_lookup_data record for each variant,
-			# and add them to the variant_lookup_data_array. 
-			# Note: A reference to the same "vcf_record" object will be stored in each Variant_lookup_data record,
-			#       however the "alt" field will contain a different ALT value.
-			variant_lookup_data_from_vcf_record(vcf_record, variant_lookup_data_array)
-
-		except StopIteration as e:
-			# Reached end of input VCF file, no new vcf_record was read
-			vcf_record = None
-
-		# If we are performing batch lookups...
-		if (do_batch_lookups):
-			# Check if we have reached (or slightly crossed) the limit of variants we want for the batch request, or the end of the input file.
-			# Note: In this implementation we may cross the limit if the last vcf_record read contained more than one variants. This is OK.
-			if (len(variant_lookup_data_array) >= _batch_limit or vcf_record is None):
-				# Extract variant strings from array.
-				variant_string_array = [vld.variant_string for vld in variant_lookup_data_array]
-
-				# Execute batch lookup request
-				batch_data = api.batch_lookup(variant_string_array, ref_genome=ref_genome, params={ 'add-all-data': 1 })
-		
-				# Process response, variant by variant
-				batch_counter = 0
-				for data in batch_data:
-					process_single_variant_response_data(variant_lookup_data_array[batch_counter], data, vcf_writer)
-					batch_counter += 1
-		
-				# Clear array
-				del variant_lookup_data_array[:]
-
-				if (vcf_record is None):
-					# Reached the end of the file, finish
-					break
-
-		# If we are performing individual lookups for each variant (which is not recommended for performance issues), 
-		# execute the lookup and process the outcome
-		else: 
-			if (vcf_record is not None):
-				# Execute lookup requests for each element in the array
-				for vld in variant_lookup_data_array:
-					data = api.lookup(vld.variant_string, ref_genome=ref_genome)
-					process_single_variant_response_data(vld, data, vcf_writer)
-
-				# Clear array
-				del variant_lookup_data_array[:]
-			else:
-				# Reached the end of the file, finish
-				break
-
-		total_counter += 1 
-		if (total_counter % 1000 == 0):
-			print ("Read ", total_counter, " rows")
-
-	print ("Finished reading ", total_counter, " rows, exiting")
-
-
-
-# Processes a vcf_record from the input VCF file, creates Variant_lookup_data objects for the variants
-# in the vcf_record, and appends them to the array variant_lookup_data_array that keeps such objects
-# for the current lookup. 
-# Input:
-#    vcf_record: The record read from the input VCF file
-#    variant_lookup_data_array: An array of Variant_lookup_data objects for the current lookup.
-# Output:
-#    None as such, but new elements are appended to the input array variant_lookup_data_array
-def variant_lookup_data_from_vcf_record(vcf_record, variant_lookup_data_array):
-	# Concatenate chromosome, position and reference, separated by ":" characters
-	variant_chromposref = vcf_record.CHROM + ":" + str(vcf_record.POS) + ":"
-	if (vcf_record.REF is not None):
-		variant_chromposref += str(vcf_record.REF)
-	variant_chromposref += ":"
-	
-	# For each ALT element, generate a new string and append to the array
-	if (vcf_record.ALT is not None):
-		for alt in vcf_record.ALT:
-			variant_string = variant_chromposref + str(alt)
-			variant_lookup_data = Variant_lookup_data(vcf_record,variant_string,alt)
-			variant_lookup_data_array.append(variant_lookup_data)
-	else:
-		variant_lookup_data = Variant_lookup_data(vcf_record,variant_chromposref,vcf_record.ALT)
-		variant_lookup_data_array.append(variant_lookup_data)
-
-
-# Processes a single variant description vcf_record and writes the resulting new record in the output VCF file
-# Input:
-#  variant_lookup_data: A Variant_lookup_data object corresponding to the variant being queried.
-#  response_data: The data received from the variant API for this specific record. Note that if the record contained more than one
-#        elements in the ALT field, and thus corresponded to more than one variants, we query the variant API once for each 
-#        variant. 
-#  vcf_writer: The output VCF file handler object
-# Output:
-#    None
-def process_single_variant_response_data(variant_lookup_data, response_data, vcf_writer):
-	# Try to extract the gene_data information from the response
-	gene_symbols = set()
-	if 'refseq_transcripts' in response_data.keys() and response_data['refseq_transcripts']:
-		for t in response_data['refseq_transcripts'][0]['items']:
-			if 'gene_symbol' in t and t['gene_symbol']:
-				gene_symbols.add(t['gene_symbol'])
-	if 'ensembl_transcripts' in response_data.keys() and response_data['ensembl_transcripts']:
-		for t in response_data['ensembl_transcripts'][0]['items']:
-			if 'gene_symbol' in t and t['gene_symbol']:
-				gene_symbols.add(t['gene_symbol'])
-
-	if gene_symbols:
-		# Concatenate all gene symbols into a comma-separated string
-		gene_str = ','.join(gene_symbols)
-
-		# Add gene entry in the INFO field, containing the string.
-		variant_lookup_data.vcf_record.INFO['GENE'] = gene_str
-
-	# Assign the correct ALT value to the vcf_record for this variant.
-	variant_lookup_data.vcf_record.ALT = [variant_lookup_data.alt_value]
-
-	# Write the record in the output vcf file.
-	vcf_writer.write_record(variant_lookup_data.vcf_record)
-
-
-if __name__ == '__main__':
-    main(argv)
diff --git a/variantapi/models/__init__.py b/variantapi/models/__init__.py
new file mode 100644
index 0000000..ee2f4d4
--- /dev/null
+++ b/variantapi/models/__init__.py
@@ -0,0 +1,3 @@
+__author__ = "ckopanos"
+
+
diff --git a/variantapi/models/elements/__init__.py b/variantapi/models/elements/__init__.py
new file mode 100644
index 0000000..276d4c7
--- /dev/null
+++ b/variantapi/models/elements/__init__.py
@@ -0,0 +1,17 @@
+__author__ = "ckopanos"
+
+from .transcript import *
+from .broad import *
+from .gnomad import *
+from .thousand_genomes import *
+from .gerp import *
+from .isb import *
+from .dbnsfp import *
+from .dann import *
+from .ncbi import *
+from .sanger import *
+from .icgc import *
+from .iarc import *
+from .uniprot import *
+from .wustl import *
+from .gwas import *
diff --git a/variantapi/models/elements/broad.py b/variantapi/models/elements/broad.py
new file mode 100644
index 0000000..467e1ca
--- /dev/null
+++ b/variantapi/models/elements/broad.py
@@ -0,0 +1,64 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class ExAC(models.Base):
+    version = fields.StringField(help_text="Version")
+    ac = fields.IntField(help_text="Allele Count", required=False, nullable=True)
+    an = fields.IntField(help_text="Allele Number", required=False, nullable=True)
+    ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True)
+    an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True)
+    af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True)
+    ac_afr = fields.IntField(help_text="Allele Count African", required=False, nullable=True)
+    ac_amr = fields.IntField(help_text="Allele Count American", required=False, nullable=True)
+    ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True)
+    ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True)
+    ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True)
+    ac_nfe = fields.IntField(help_text="Allele Count European (Non-Finnish)", required=False, nullable=True)
+    ac_oth = fields.IntField(help_text="Allele Count Other", required=False, nullable=True)
+    ac_sas = fields.IntField(help_text="Allele Count South Asian", required=False, nullable=True)
+    ac_male = fields.IntField(help_text="Allele Count Male", required=False, nullable=True)
+    ac_female = fields.IntField(help_text="Allele Count Female", required=False, nullable=True)
+    hom = fields.IntField(help_text="Number of Homozygotes", required=False, nullable=True)
+    hemi = fields.IntField(help_text="Number of Hemizygotes", required=False, nullable=True)
+    ac_hom = fields.FloatField(help_text="Number of Homozygotes", required=False, nullable=True)
+    ac_hemi = fields.FloatField(help_text="Number of Hemizygotes", required=False, nullable=True)
+    an_afr = fields.IntField(help_text="Allele Number African", required=False, nullable=True)
+    an_amr = fields.IntField(help_text="Allele Number American", required=False, nullable=True)
+    an_asj = fields.IntField(help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True)
+    an_eas = fields.IntField(help_text="Allele Number East Asian", required=False, nullable=True)
+    an_fin = fields.IntField(help_text="Allele Number European (Finnish)", required=False, nullable=True)
+    an_nfe = fields.IntField(help_text="Allele Number European (Non-Finnish)", required=False, nullable=True)
+    an_oth = fields.IntField(help_text="Allele Number Other", required=False, nullable=True)
+    an_sas = fields.IntField(help_text="Allele Number South Asian", required=False, nullable=True)
+    an_male = fields.IntField(help_text="Allele Number Male", required=False, nullable=True)
+    an_female = fields.IntField(help_text="Allele Number Female", required=False, nullable=True)
+    hom_afr = fields.IntField(help_text="Number of Homozygotes African", required=False, nullable=True)
+    hom_amr = fields.IntField(help_text="Number of Homozygotes American", required=False, nullable=True)
+    hom_asj = fields.IntField(help_text="Number of Homozygotes Ashkenazi Jewish", required=False, nullable=True)
+    hom_eas = fields.IntField(help_text="Number of Homozygotes East Asian", required=False, nullable=True)
+    hom_fin = fields.IntField(help_text="Number of Homozygotes European (Finnish)", required=False, nullable=True)
+    hom_nfe = fields.IntField(help_text="Number of Homozygotes European (Non-Finnish)", required=False, nullable=True)
+    hom_oth = fields.IntField(help_text="Number of Homozygotes Other", required=False, nullable=True)
+    hom_sas = fields.IntField(help_text="Number of Homozygotes South Asian", required=False, nullable=True)
+    hom_male = fields.IntField(help_text="Number of Homozygotes Male", required=False, nullable=True)
+    hom_female = fields.IntField(help_text="Number of Homozygotes Female", required=False, nullable=True)
+    hemi_afr = fields.IntField(help_text="Number of Hemizygotes African", required=False, nullable=True)
+    hemi_amr = fields.IntField(help_text="Number of Hemizygotes American", required=False, nullable=True)
+    hemi_asj = fields.IntField(help_text="Number of Hemizygotes Ashkenazi Jewish", required=False, nullable=True)
+    hemi_eas = fields.IntField(help_text="Number of Hemizygotes East Asian", required=False, nullable=True)
+    hemi_fin = fields.IntField(help_text="Number of Hemizygotes European (Finnish)", required=False, nullable=True)
+    hemi_nfe = fields.IntField(help_text="Number of Hemizygotes European (Non-Finnish)", required=False, nullable=True)
+    hemi_oth = fields.IntField(help_text="Number of Hemizygotes Other", required=False, nullable=True)
+    hemi_sas = fields.IntField(help_text="Number of Hemizygotes South Asian", required=False, nullable=True)
+    af_afr = fields.FloatField(help_text="Allele Frequency African", required=False, nullable=True)
+    af_amr = fields.FloatField(help_text="Allele Frequency American", required=False, nullable=True)
+    af_asj = fields.FloatField(help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True)
+    af_eas = fields.FloatField(help_text="Allele Frequency East Asian", required=False, nullable=True)
+    af_fin = fields.FloatField(help_text="Allele Frequency European (Finnish)", required=False, nullable=True)
+    af_nfe = fields.FloatField(help_text="Allele Frequency European (Non-Finnish)", required=False, nullable=True)
+    af_oth = fields.FloatField(help_text="Allele Frequency Other", required=False, nullable=True)
+    af_sas = fields.FloatField(help_text="Allele Frequency South Asian", required=False, nullable=True)
+    af_male = fields.FloatField(help_text="Allele Frequency Male", required=False, nullable=True)
+    af_female = fields.FloatField(help_text="Allele Frequency Female", required=False, nullable=True)
\ No newline at end of file
diff --git a/variantapi/models/elements/dann.py b/variantapi/models/elements/dann.py
new file mode 100644
index 0000000..6913d94
--- /dev/null
+++ b/variantapi/models/elements/dann.py
@@ -0,0 +1,8 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class DannSNVs(models.Base):
+    version = fields.StringField(help_text="Version")
+    dann_score = fields.FloatField(help_text="DANN Score", required=False, nullable=True)
diff --git a/variantapi/models/elements/dbnsfp.py b/variantapi/models/elements/dbnsfp.py
new file mode 100644
index 0000000..df79a90
--- /dev/null
+++ b/variantapi/models/elements/dbnsfp.py
@@ -0,0 +1,110 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class DbNSFP(models.Base):
+    version = fields.StringField(help_text="Version")
+    mutationtaster_pred = fields.ListField(items_types=(str,), help_text="MutationTaster Prediction",
+                                           required=False)
+    mutationtaster_score = fields.ListField(items_types=(float,),
+                                            help_text="MutationTaster Accuracy", required=False, nullable=True)
+    sift_score = fields.ListField(items_types=(float,), help_text="SIFT score", required=False, nullable=True)
+    sift_prediction = fields.StringField(help_text="SIFT prediction", required=False, nullable=True)
+    phylop100way_vertebrate = fields.ListField(items_types=(float,), help_text="phyloP100way vertebrate",
+                                               required=False)
+    phylop46way_placental = fields.ListField(items_types=(float,), help_text="phyloP46way placental",
+                                             required=False)
+    phylop46way_primate = fields.ListField(items_types=(float,), help_text="phyloP46way primate",
+                                           required=False)
+    mutationtaster_converted_rankscore = fields.ListField(items_types=(float,),
+                                                          help_text="MutationTaster converted rankscore",
+                                                          required=False, nullable=True)
+    mutationassessor_pred = fields.ListField(items_types=(str,),
+                                             help_text="MutationAssessor prediction",
+                                             required=False)
+    mutationassessor_score = fields.ListField(items_types=(float,), help_text="MutationAssessor score",
+                                              required=False)
+    mutationassessor_score_rankscore = fields.ListField(items_types=(float,),
+                                                        help_text="MutationAssessor rankscore", required=False,
+                                                        nullable=True)
+    fathmm_mkl_coding_pred = fields.ListField(items_types=(str,),
+                                              help_text="FATHMM-MKL coding prediction", required=False, nullable=True)
+    fathmm_mkl_coding_score = fields.ListField(items_types=(float,), help_text="FATHMM-MKL coding score",
+                                               required=False)
+    fathmm_mkl_coding_rankscore = fields.ListField(items_types=(float,),
+                                                   help_text="FATHMM-MKL coding rankscore", required=False,
+                                                   nullable=True)
+    fathmm_pred = fields.ListField(items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True)
+    fathmm_score = fields.ListField(items_types=(float,), help_text="FATHMM score",
+                                    required=False)
+    fathmm_converted_rankscore = fields.ListField(items_types=(float,), help_text="FATHMM converted rankscore",
+                                                  required=False, nullable=True)
+    sift_converted_rankscore = fields.ListField(items_types=(float,), help_text="SIFT converted rankscore",
+                                                required=False)
+    metasvm_pred = fields.ListField(items_types=(str,), help_text="MetaSVM prediction",
+                                    required=False)
+    metasvm_score = fields.ListField(items_types=(float,), help_text="MetaSVM score", required=False, nullable=True)
+    metasvm_rankscore = fields.ListField(items_types=(float,), help_text="MetaSVM rankscore",
+                                         required=False)
+    metalr_pred = fields.ListField(items_types=(str,), help_text="MetalR prediction", required=False, nullable=True)
+    metalr_score = fields.ListField(items_types=(float,), help_text="MetalR score", required=False, nullable=True)
+    metalr_rankscore = fields.ListField(items_types=(float,), help_text="MetalR rankscore", required=False,
+                                        nullable=True)
+    provean_pred = fields.ListField(items_types=(str,), help_text="Provean prediction",
+                                    required=False)
+    provean_score = fields.ListField(items_types=(float,), help_text="Provean score",
+                                     required=False)
+    provean_converted_rankscore = fields.ListField(items_types=(float,),
+                                                   help_text="Provean converted rankscore", required=False,
+                                                   nullable=True)
+    lrt_pred = fields.ListField(items_types=(str,), help_text="LRT prediction", required=False, nullable=True)
+    lrt_score = fields.ListField(items_types=(float,), help_text="LRT score", required=False, nullable=True)
+    lrt_converted_rankscore = fields.ListField(items_types=(float,), help_text="LRT converted rankscore",
+                                               required=False)
+    lrt_omega = fields.ListField(items_types=(float,), help_text="LRT Omega", required=False, nullable=True)
+    cadd_raw = fields.ListField(items_types=(float,), help_text="CADD raw score", required=False, nullable=True)
+    cadd_raw_rankscore = fields.ListField(items_types=(float,), help_text="CADD raw rankscore",
+                                          required=False)
+    cadd_phred = fields.ListField(items_types=(float,), help_text="CADD phred", required=False, nullable=True)
+    gm12878_confidence_value = fields.ListField(items_types=(float,),
+                                                help_text="GM12878 fitCons confidence value", required=False,
+                                                nullable=True)
+    gm12878_fitcons_score = fields.ListField(items_types=(float,), help_text="GM12878 fitCons score",
+                                             required=False)
+    gm12878_fitcons_score_rankscore = fields.ListField(items_types=(float,),
+                                                       help_text="GM12878 fitCons rankscore", required=False,
+                                                       nullable=True)
+    siphy_29way_logodds_rankscore = fields.ListField(items_types=(float,),
+                                                     help_text="SiPhy29way logOdds rankscore", required=False,
+                                                     nullable=True)
+    siphy_29way_pi = fields.ListField(items_types=(float,),
+                                      help_text="SiPhy29way pi", required=False, nullable=True)
+    phylop20way_mammalian = fields.ListField(items_types=(float,), help_text="phyloP20way mammalian",
+                                             required=False)
+    phylop20way_mammalian_rankscore = fields.ListField(items_types=(float,),
+                                                       help_text="phyloP20way mammalian rankscore", required=False,
+                                                       nullable=True)
+    phylop100way_vertebrate_rankscore = fields.ListField(items_types=(float,),
+                                                         help_text="phyloP100way vertebrate rankscore", required=False,
+                                                         nullable=True)
+    phastcons20way_mammalian = fields.ListField(items_types=(float,), help_text="phastCons20way mammalian",
+                                                required=False)
+    phastcons20way_mammalian_rankscore = fields.ListField(items_types=(float,),
+                                                          help_text="phastCons20way mammalian rankscore",
+                                                          required=False, nullable=True)
+    phastcons100way_vertebrate = fields.ListField(items_types=(float,),
+                                                  help_text="phastCons100way vertebrate", required=False, nullable=True)
+    phastcons100way_vertebrate_rankscore = fields.ListField(items_types=(float,),
+                                                            help_text="phastCons100way vertebrate rankscore",
+                                                            required=False, nullable=True)
+    vest3_score = fields.ListField(items_types=(float,), help_text="VEST3 score",
+                                   required=False)
+    vest3_rankscore = fields.ListField(items_types=(float,),
+                                       help_text="VEST3 rankscore", required=False, nullable=True)
+
+
+class DBscSNV(models.Base):
+    version = fields.StringField(help_text="Version")
+    ada_score = fields.ListField(items_types=(float, ), help_text='ADA Score', required=False, nullable=True)
+    rf_score = fields.ListField(items_types=(float,), help_text='RF Score', required=False, nullable=True)
\ No newline at end of file
diff --git a/variantapi/models/elements/gerp.py b/variantapi/models/elements/gerp.py
new file mode 100644
index 0000000..3d6b02e
--- /dev/null
+++ b/variantapi/models/elements/gerp.py
@@ -0,0 +1,9 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class Gerp(models.Base):
+    version = fields.StringField(help_text="Version")
+    gerp_nr = fields.ListField(items_types=(float, type(None)), required=False, help_text="GERP NR", nullable=True)
+    gerp_rs = fields.ListField(items_types=(float, type(None)), required=False, help_text="GERP RS", nullable=True)
diff --git a/variantapi/models/elements/gnomad.py b/variantapi/models/elements/gnomad.py
new file mode 100644
index 0000000..7336598
--- /dev/null
+++ b/variantapi/models/elements/gnomad.py
@@ -0,0 +1,64 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class GnomADCoverage(models.Base):
+    version = fields.StringField(help_text="Version")
+    coverage_mean = fields.ListField(help_text="Mean coverage",
+                                     items_types=(float, type(None)), required=False, nullable=True)
+    coverage_median = fields.ListField(help_text="Median coverage",
+                                       items_types=(float, type(None)), required=False, nullable=True)
+    coverage_20_frequency = fields.ListField(help_text="Proportion of samples with over 20x",
+                                             items_types=(float, type(None)),
+                                             required=False, nullable=True)
+
+
+class GnomAD(models.Base):
+    version = fields.StringField(help_text="Version")
+    ac = fields.IntField(help_text="Allele Count", required=False, nullable=True)
+    an = fields.IntField(help_text="Allele Number", required=False, nullable=True)
+    ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True)
+    an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True)
+    af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True)
+    ac_afr = fields.IntField(help_text="Allele Count African", required=False, nullable=True)
+    ac_amr = fields.IntField(help_text="Allele Count American", required=False, nullable=True)
+    ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True)
+    ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True)
+    ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True)
+    ac_nfe = fields.IntField(help_text="Allele Count European (Non-Finnish)", required=False, nullable=True)
+    ac_oth = fields.IntField(help_text="Allele Count Other", required=False, nullable=True)
+    ac_male = fields.IntField(help_text="Allele Count Male", required=False, nullable=True)
+    ac_female = fields.IntField(help_text="Allele Count Female", required=False, nullable=True)
+    hom = fields.IntField(help_text="Number of Homozygotes", required=False, nullable=True)
+    hemi = fields.IntField(help_text="Number of Hemizygotes", required=False, nullable=True)
+    ac_hom = fields.FloatField(help_text="Number of Homozygotes", required=False, nullable=True)
+    ac_hemi = fields.FloatField(help_text="Number of Hemizygotes", required=False, nullable=True)
+    an_afr = fields.IntField(help_text="Allele Number African", required=False, nullable=True)
+    an_amr = fields.IntField(help_text="Allele Number American", required=False, nullable=True)
+    an_asj = fields.IntField(help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True)
+    an_eas = fields.IntField(help_text="Allele Number East Asian", required=False, nullable=True)
+    an_fin = fields.IntField(help_text="Allele Number European (Finnish)", required=False, nullable=True)
+    an_nfe = fields.IntField(help_text="Allele Number European (Non-Finnish)", required=False, nullable=True)
+    an_oth = fields.IntField(help_text="Allele Number Other", required=False, nullable=True)
+    an_male = fields.IntField(help_text="Allele Number Male", required=False, nullable=True)
+    an_female = fields.IntField(help_text="Allele Number Female", required=False, nullable=True)
+    hom_afr = fields.IntField(help_text="Number of Homozygotes African", required=False, nullable=True)
+    hom_amr = fields.IntField(help_text="Number of Homozygotes American", required=False, nullable=True)
+    hom_asj = fields.IntField(help_text="Number of Homozygotes Ashkenazi Jewish", required=False, nullable=True)
+    hom_eas = fields.IntField(help_text="Number of Homozygotes East Asian", required=False, nullable=True)
+    hom_fin = fields.IntField(help_text="Number of Homozygotes European (Finnish)", required=False, nullable=True)
+    hom_nfe = fields.IntField(help_text="Number of Homozygotes European (Non-Finnish)", required=False, nullable=True)
+    hom_oth = fields.IntField(help_text="Number of Homozygotes Other", required=False, nullable=True)
+    hom_male = fields.IntField(help_text="Number of Homozygotes Male", required=False, nullable=True)
+    hom_female = fields.IntField(help_text="Number of Homozygotes Female", required=False, nullable=True)
+    af_afr = fields.FloatField(help_text="Allele Frequency African", required=False, nullable=True)
+    af_amr = fields.FloatField(help_text="Allele Frequency American", required=False, nullable=True)
+    af_asj = fields.FloatField(help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True)
+    af_eas = fields.FloatField(help_text="Allele Frequency East Asian", required=False, nullable=True)
+    af_fin = fields.FloatField(help_text="Allele Frequency European (Finnish)", required=False, nullable=True)
+    af_nfe = fields.FloatField(help_text="Allele Frequency European (Non-Finnish)", required=False, nullable=True)
+    af_oth = fields.FloatField(help_text="Allele Frequency Other", required=False, nullable=True)
+    af_male = fields.FloatField(help_text="Allele Frequency Male", required=False, nullable=True)
+    af_female = fields.FloatField(help_text="Allele Frequency Female", required=False, nullable=True)
+    main_data = fields.StringField(help_text="Main data point", required=False, nullable=True)
diff --git a/variantapi/models/elements/gwas.py b/variantapi/models/elements/gwas.py
new file mode 100644
index 0000000..937409c
--- /dev/null
+++ b/variantapi/models/elements/gwas.py
@@ -0,0 +1,28 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class GWASDetails(models.Base):
+    gwas_symbol = fields.StringField(help_text="GWAS symbol", required=False, nullable=True)
+    date = fields.StringField(help_text="Date", required=False, nullable=True)
+    study = fields.StringField(help_text="Study", required=False, nullable=True)
+    disease_or_trait = fields.StringField(help_text="Disease or trait", required=False, nullable=True)
+    mapped_traits = fields.ListField(items_types=(str,), help_text="Mapped trait", required=False, nullable=True)
+    mapped_trait_urls = fields.ListField(items_types=(str,), help_text="Mapped trait URL", required=False,
+                                         nullable=True)
+    strongest_snp_risk_allele = fields.StringField(help_text="Strongest SNP risk allele", required=False, nullable=True)
+    odds_ratio = fields.FloatField(help_text="Odds ratio", required=False, nullable=True)
+    p_value = fields.StringField(help_text="p value", required=False, nullable=True)
+    confidence_range_95_low = fields.FloatField(help_text="Confidence range 95% low", required=False, nullable=True)
+    confidence_range_95_high = fields.FloatField(help_text="Confidence range 95% high", required=False, nullable=True)
+    confidence_comment = fields.StringField(help_text="Confidence comment", required=False, nullable=True)
+    initial_sample_size = fields.StringField(help_text="Initial sample size", required=False, nullable=True)
+    replication_sample_size = fields.StringField(help_text="Replication sample size", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed References", required=False,
+                                          nullable=True)
+
+
+class GWAS(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(help_text='Details', items_types=(GWASDetails,))
diff --git a/variantapi/models/elements/iarc.py b/variantapi/models/elements/iarc.py
new file mode 100644
index 0000000..0263d12
--- /dev/null
+++ b/variantapi/models/elements/iarc.py
@@ -0,0 +1,41 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class TP53GermlineDetails(models.Base):
+    age_at_diagnosis = fields.IntField(help_text="Age at diagnosis", required=False, nullable=True)
+    country = fields.StringField(help_text="Country", required=False, nullable=True)
+    effect = fields.StringField(help_text="Effect", required=False, nullable=True)
+    familycase = fields.StringField(help_text="Family case", required=False, nullable=True)
+    familycase_group = fields.StringField(help_text="Family case group", required=False, nullable=True)
+    family_code = fields.StringField(help_text="Family code", required=False, nullable=True)
+    generation = fields.StringField(help_text="Generation", required=False, nullable=True)
+    morphology = fields.StringField(help_text="Morphology", required=False, nullable=True)
+    sex = fields.StringField(help_text="Sex", required=False, nullable=True)
+    topography = fields.StringField(help_text="Topography", required=False, nullable=True)
+    unaffected = fields.IntField(help_text="Unaffected", required=False, nullable=True)
+
+
+class TP53SomaticDetails(models.Base):
+    age = fields.IntField(help_text="Age", required=False, nullable=True)
+    country = fields.StringField(help_text="Country", required=False, nullable=True)
+    effect = fields.StringField(help_text="Effect", required=False, nullable=True)
+    morphology = fields.StringField(help_text="Morphology", required=False, nullable=True)
+    mut_rate = fields.IntField(help_text="Mutation rate", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed References", required=False,
+                                          nullable=True)
+    sample_source = fields.StringField(help_text="Sample source", required=False, nullable=True)
+    stage = fields.StringField(help_text="Stage", required=False, nullable=True)
+    structural_motif = fields.StringField(help_text="Structural Motif", required=False, nullable=True)
+    topography = fields.StringField(help_text="Topography", required=False, nullable=True)
+
+
+class TP53Germline(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(help_text='Details', items_types=(TP53GermlineDetails,))
+
+
+class TP53Somatic(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(help_text='Details', items_types=(TP53SomaticDetails,))
diff --git a/variantapi/models/elements/icgc.py b/variantapi/models/elements/icgc.py
new file mode 100644
index 0000000..903f037
--- /dev/null
+++ b/variantapi/models/elements/icgc.py
@@ -0,0 +1,18 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class Occurrence(models.Base):
+    affected = fields.IntField(required=False, nullable=True, help_text="Affected number")
+    donors = fields.IntField(required=False, nullable=True, help_text="Donors number")
+    project = fields.StringField(required=False, nullable=True, help_text="Project")
+
+
+class Somatic(models.Base):
+    version = fields.StringField(help_text="Version")
+    id = fields.StringField(help_text="ID", required=False, nullable=True)
+    occurrence = fields.ListField(required=False, nullable=True, items_types=(Occurrence, ), help_text="Occurrence")
+    affected_donors = fields.IntField(help_text="Affected Donors", required=False, nullable=True)
+    project_count = fields.IntField(help_text="Project Count", required=False, nullable=True)
+    main_data = fields.StringField(help_text="Main data point", required=False, nullable=True)
\ No newline at end of file
diff --git a/variantapi/models/elements/isb.py b/variantapi/models/elements/isb.py
new file mode 100644
index 0000000..ae75a29
--- /dev/null
+++ b/variantapi/models/elements/isb.py
@@ -0,0 +1,10 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class Kaviar3(models.Base):
+    version = fields.StringField(help_text="Version")
+    ac = fields.ListField(items_types=(int, ), help_text="ac", required=False, nullable=True)
+    an = fields.ListField(items_types=(int,), help_text="an", required=False, nullable=True)
+    main_data = fields.StringField(help_text="Main data point", required=False)
\ No newline at end of file
diff --git a/variantapi/models/elements/ncbi.py b/variantapi/models/elements/ncbi.py
new file mode 100644
index 0000000..8dcbb9f
--- /dev/null
+++ b/variantapi/models/elements/ncbi.py
@@ -0,0 +1,44 @@
+from jsonmodels import models, fields
+
+from variantapi.models.fields import DictField
+
+__author__ = "ckopanos"
+
+
+class DbSNP(models.Base):
+    version = fields.StringField(help_text="Version")
+    rsid = fields.ListField(items_types=(int,), help_text="RS ID")
+
+
+class ClinVarDisease(models.Base):
+    clndbn = fields.StringField(help_text="Disease", required=False, nullable=True)
+    clnsig = fields.IntField(help_text="Clinical Significance", required=False, nullable=True)
+    databases = DictField(help_text="External links",
+                          required=False, )  # todo specify the types of databases and assorted values
+    clnsig_description = fields.StringField(help_text="Clinical Significance description", required=False,
+                                            nullable=True)
+
+
+class ClinVar(models.Base):
+    version = fields.StringField(help_text="Version")
+    clnorigin = fields.IntField(required=False, nullable=True, help_text="Allele Origin")
+    clnorigin_description = fields.StringField(help_text="Allele Origin description", required=False, nullable=True)
+    disease = fields.ListField(items_types=(ClinVarDisease,), help_text="Disease", nullable=True, required=False)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed references", required=False,
+                                          nullable=True)
+
+
+class ClinVar2(models.Base):
+    version = fields.StringField(help_text="Version")
+    review_status = fields.StringField(help_text="Review status", required=False, nullable=True)
+    review_stars = fields.IntField(help_text="Review stars", required=False, nullable=True)
+    variation_id = fields.IntField(help_text="Variation ID", required=False, nullable=True)
+    num_submitters = fields.IntField(help_text="Number of submitters", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed references", required=False,
+                                          nullable=True)
+    clinical_significance = fields.ListField(items_types=(str,), help_text="Clinical significance", required=False,
+                                             nullable=True)
+    last_evaluation = fields.StringField(help_text="Last evaluation", required=False, nullable=True)
+    origin = fields.ListField(items_types=(str,), help_text="Origin", required=False, nullable=True)
+    accessions = fields.ListField(items_types=(dict,), help_text="Accessions", required=False, nullable=True)
+    main_data = fields.StringField(help_text="Main data point", required=False, nullable=True)
diff --git a/variantapi/models/elements/sanger.py b/variantapi/models/elements/sanger.py
new file mode 100644
index 0000000..18f6265
--- /dev/null
+++ b/variantapi/models/elements/sanger.py
@@ -0,0 +1,82 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class Cosmic(models.Base):
+    version = fields.StringField(help_text="Version")
+    primary_site = fields.ListField(items_types=(str,), help_text="Primary site", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False,
+                                          nullable=True)
+
+
+class CosmicLicensedDrugEntry(models.Base):
+    drug_name = fields.StringField(help_text="Drug name", required=False, nullable=True)
+    somatic_status = fields.StringField(help_text="Somatic status", required=False, nullable=True)
+    zygosity = fields.StringField(help_text="Zygosity", required=False, nullable=True)
+    gene = fields.StringField(help_text="Gene", required=False, nullable=True)
+    transcript = fields.StringField(help_text="Transcript", required=False, nullable=True)
+    census_gene = fields.StringField(help_text="Census gene", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False,
+                                          nullable=True)
+    histology_freq = fields.ListField(items_types=(float,), help_text="Histology frequency", required=False,
+                                      nullable=True)
+    tissue_freq = fields.ListField(items_types=(float,), help_text="Tissue frequency", required=False, nullable=True)
+
+
+class CosmicLicensedDetails(models.Base):
+    entry_type = fields.StringField(help_text="Entry type", required=False, nullable=True)
+    cosmic_id = fields.ListField(items_types=(str,), help_text="Cosmic ID", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False,
+                                          nullable=True)
+    histology_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False,
+                                      nullable=True)
+    genome_wide_screen_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False,
+                                               nullable=True)
+    loh_freq = fields.ListField(items_types=(int, str, float), help_text="LOH frequency", required=False, nullable=True)
+    age_freq = fields.ListField(items_types=(int, str, float), help_text="Age frequency", required=False, nullable=True)
+    zygosity_freq = fields.ListField(items_types=(int, str, float), help_text="Zygosity frequency", required=False,
+                                     nullable=True)
+    tumour_origin_freq = fields.ListField(items_types=(int, str, float,), help_text="Tumour original frequency", required=False,
+                                          nullable=True)
+    somatic_status_freq = fields.ListField(items_types=(int, str, float), help_text="Somatic status frequency", required=False,
+                                           nullable=True)
+    primary_site_freq = fields.ListField(items_types=(int, str, float), help_text="Primary site frequency", required=False, nullable=True)
+    description = fields.ListField(items_types=(str,), help_text="Description", required=False, nullable=True)
+    accession_number = fields.ListField(items_types=(str,), help_text="Accession number", required=False, nullable=True)
+    fathmm_prediction = fields.StringField(help_text="FATHMM prediction", required=False, nullable=True)
+    fathmm_score = fields.FloatField(help_text="FATHMM score", required=False, nullable=True)
+    num_entries = fields.IntField(help_text="Number of entries", required=False, nullable=True)
+    num_samples = fields.IntField(help_text="Number of samples", required=False, nullable=True)
+    gene = fields.ListField(items_types=(str,), help_text="Gene", required=False, nullable=True)
+
+    fathmm_mkl_coding_score = fields.FloatField(help_text="FATHMM_MKL coding score", required=False, nullable=True)
+    fathmm_mkl_coding_groups = fields.StringField(help_text="FATHMM_MKL coding groups", required=False, nullable=True)
+    fathmm_mkl_non_coding_score = fields.FloatField(help_text="FATHMM_MKL non coding score", required=False,
+                                                    nullable=True)
+    fathmm_mkl_non_coding_groups = fields.StringField(help_text="FATHMM_MKL non coding groups", required=False,
+                                                      nullable=True)
+    whole_exome_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole exome frequency", required=False,
+                                        nullable=True)
+    whole_genome_reseq_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole genome reseq frequency",
+                                               required=False, nullable=True)
+
+    resistance_mutation = fields.ListField(items_types=(str,), help_text="Resistance mutation", required=False,
+                                           nullable=True)
+    drug_entries = fields.ListField(items_types=(CosmicLicensedDrugEntry,), help_text="Drug entries", required=False,
+                                    nullable=True)
+
+
+class ComsicPublicDetails(models.Base):
+    num_samples = fields.IntField(help_text='Number of samples')
+    id = fields.StringField(help_text='Cosmic ID')
+
+
+class CosmicPublic(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(items_types=(ComsicPublicDetails, ), help_text="Details", required=False, nullable=True)
+
+
+class CosmicLicensed(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(items_types=(CosmicLicensedDetails,), help_text="Details")
diff --git a/variantapi/models/elements/thousand_genomes.py b/variantapi/models/elements/thousand_genomes.py
new file mode 100644
index 0000000..ea9c618
--- /dev/null
+++ b/variantapi/models/elements/thousand_genomes.py
@@ -0,0 +1,21 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class ThousandGenomes(models.Base):
+    version = fields.StringField(help_text="Version")
+    ac = fields.ListField(items_types=(int,), help_text="Allele Count", required=False, nullable=True)
+    af = fields.ListField(items_types=(float,), help_text="Allele Frequency", required=False, nullable=True)
+    an = fields.ListField(items_types=(int,), help_text="Allele Number", required=False, nullable=True)
+    ns = fields.ListField(items_types=(int,), help_text="Number of Samples", required=False, nullable=True)
+    afr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency African", required=False, nullable=True)
+    amr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency American", required=False,
+                              nullable=True)
+    eas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency East Asian", required=False,
+                              nullable=True)
+    eur_af = fields.ListField(items_types=(float,), help_text="Allele Frequency European", required=False,
+                              nullable=True)
+    sas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency South Asian", required=False,
+                              nullable=True)
+    main_data = fields.StringField(help_text="Main data point", required=False, nullable=True)
diff --git a/variantapi/models/elements/transcript.py b/variantapi/models/elements/transcript.py
new file mode 100644
index 0000000..7a19918
--- /dev/null
+++ b/variantapi/models/elements/transcript.py
@@ -0,0 +1,22 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class TranscriptItem(models.Base):
+    name = fields.StringField(help_text="Transcript")
+    coding_impact = fields.StringField(help_text="Coding impact", required=False, nullable=True)
+    function = fields.ListField(help_text="Function", items_types=(str,), required=False, nullable=True)
+    hgvs = fields.StringField(required=False, help_text="HGVS cDNA level", nullable=True)
+    hgvs_p1 = fields.StringField(required=False, nullable=True)
+    hgvs_p3 = fields.StringField(required=False, nullable=True)
+    hgvs_notation = fields.StringField(help_text="HGVS notation", required=False, nullable=True)
+    location = fields.StringField(help_text="Location", required=False, nullable=True)
+    coding_location = fields.StringField(help_text="Coding location", required=False, nullable=True)
+    canonical = fields.BoolField(help_text="Canonical", required=False, nullable=True)
+    gene_symbol = fields.StringField(help_text="Gene symbol", required=False, nullable=True)
+
+
+class Transcript(models.Base):
+    items = fields.ListField(help_text='Transcripts', items_types=(TranscriptItem,), required=False)
+    version = fields.StringField(help_text="Version")
diff --git a/variantapi/models/elements/uniprot.py b/variantapi/models/elements/uniprot.py
new file mode 100644
index 0000000..70b84f9
--- /dev/null
+++ b/variantapi/models/elements/uniprot.py
@@ -0,0 +1,21 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class UniprotVariantsDetails(models.Base):
+    annotation_id = fields.StringField(help_text="Annotation ID", required=False, nullable=True)
+    protein_id = fields.StringField(help_text="Protein ID", required=False, nullable=True)
+    bed_comments = fields.ListField(help_text="Comments", items_types=(str, ), required=False, nullable=True)
+    gene = fields.StringField(help_text="Gene", required=False, nullable=True)
+    variant_type = fields.StringField(help_text="Variant type", required=False, nullable=True)
+    transcripts = fields.ListField(help_text="Transcripts", items_types=(str,), required=False, nullable=True)
+    pub_med_references = fields.ListField(help_text="PubMed References", items_types=(int,), required=False, nullable=True)
+    disease = fields.StringField(help_text="Disease", required=False, nullable=True)
+    disease_symbol = fields.StringField(help_text="Disease symbol", required=False, nullable=True)
+    disease_alt_symbol = fields.StringField(help_text="Disease alt symbol", required=False, nullable=True)
+
+
+class UniprotVariants(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(help_text='Details', items_types=(UniprotVariantsDetails,))
diff --git a/variantapi/models/elements/wustl.py b/variantapi/models/elements/wustl.py
new file mode 100644
index 0000000..09aa90e
--- /dev/null
+++ b/variantapi/models/elements/wustl.py
@@ -0,0 +1,32 @@
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class CivicDetails(models.Base):
+    variant = fields.StringField(help_text="Variant", required=False, nullable=True)
+    variant_summary = fields.StringField(help_text="Variant summary", required=False, nullable=True)
+    variant_civic_url = fields.StringField(help_text="Variant CIViC URL", required=False, nullable=True)
+    variant_origin = fields.StringField(help_text="Variant origin", required=False, nullable=True)
+    pub_med_references = fields.ListField(items_types=(int, ), help_text="PubMed References", required=False, nullable=True)
+    clinical_significance = fields.StringField(help_text="Clinical significance", required=False, nullable=True)
+    evidence_level = fields.StringField(help_text="Evidence level", required=False, nullable=True)
+    evidence_statement = fields.StringField(help_text="Evidence statement", required=False, nullable=True)
+    evidence_type = fields.StringField(help_text="Evidence type", required=False, nullable=True)
+    evidence_status = fields.StringField(help_text="Evidence status", required=False, nullable=True)
+    evidence_direction = fields.StringField(help_text="Evidence direction", required=False, nullable=True)
+    evidence_civic_url = fields.StringField(help_text="Evidence CIViC URL", required=False, nullable=True)
+    drugs = fields.ListField(items_types=(str, ), help_text="Drugs", required=False, nullable=True)
+    transcripts = fields.ListField(items_types=(str, ), help_text="Transcripts", required=False, nullable=True)
+    representative_transcript = fields.StringField(help_text="Representative transcript", required=False, nullable=True)
+    disease = fields.StringField(help_text="Disease", required=False, nullable=True)
+    rating = fields.StringField(help_text="Rating", required=False, nullable=True)
+    gene = fields.StringField(help_text="Gene", required=False, nullable=True)
+    gene_civic_url = fields.StringField(help_text="Gene CIViC URL", required=False, nullable=True)
+    entrez_id = fields.StringField(help_text="Entrez ID", required=False, nullable=True)
+    doid = fields.StringField(help_text="DOID", required=False, nullable=True)
+
+
+class Civic(models.Base):
+    version = fields.StringField(help_text="Version")
+    items = fields.ListField(help_text='Details', items_types=(CivicDetails, ))
\ No newline at end of file
diff --git a/variantapi/models/fields.py b/variantapi/models/fields.py
new file mode 100644
index 0000000..5fc924c
--- /dev/null
+++ b/variantapi/models/fields.py
@@ -0,0 +1,9 @@
+from jsonmodels import fields
+
+__author__ = "ckopanos"
+
+
+class DictField(fields.BaseField):
+
+    types = (dict,)
+
diff --git a/variantapi/models/variant.py b/variantapi/models/variant.py
new file mode 100644
index 0000000..a943884
--- /dev/null
+++ b/variantapi/models/variant.py
@@ -0,0 +1,47 @@
+from .elements import *
+
+__author__ = "ckopanos"
+
+class AnnotatedVariant(models.Base):
+
+    chromosome = fields.StringField(help_text="Chromosome")
+    alt = fields.StringField(help_text="ALT Sequence", required=False, nullable=True)
+    ref = fields.StringField(help_text="REF Sequence", required=False, nullable=True)
+    pos = fields.IntField(help_text="Position")
+    variant_id = fields.StringField(help_text='Variant Id')
+    refseq_transcripts = fields.ListField(required=False, items_types=(Transcript, ), help_text="RefSeq Transcripts")
+    ensembl_transcripts = fields.ListField(required=False, items_types=(Transcript,), help_text="Ensembl Transcripts")
+    broad_exac = fields.ListField(required=False, items_types=(ExAC,), help_text="ExAC")
+    gnomad_exomes = fields.ListField(required=False, items_types=(GnomAD, ), help_text="gnomAD Exomes (ExAC)")
+    gnomad_exomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage, ), help_text="gnomAD exomes coverage")
+    gnomad_genomes = fields.ListField(required=False, items_types=(GnomAD,), help_text="gnomAD Genomes")
+    gnomad_genomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage,), help_text="gnomAD genomes coverage")
+    thousand_genomes = fields.ListField(required=False, items_types=(ThousandGenomes, ), help_text="1000 Genomes")
+    gerp = fields.ListField(required=False, items_types=(Gerp,), help_text="GERP")
+    isb_kaviar3 = fields.ListField(required=False, items_types=(Kaviar3, ), help_text='ISB Kaviar3')
+    dbnsfp = fields.ListField(required=False, items_types=(DbNSFP, ), help_text="dbNSFP")
+    dann_snvs = fields.ListField(required=False, items_types=(DannSNVs, ), help_text="DANN score")
+    dbnsfp_dbscsnv = fields.ListField(required=False, items_types=(DBscSNV, ), help_text='dbNSFP dbscSNV')
+    ncbi_dbsnp = fields.ListField(required=False, items_types=(DbSNP, ), help_text="dbSNP")
+    sanger_cosmic = fields.ListField(required=False, items_types=(Cosmic, ), help_text="Sanger Cosmic")
+    sanger_cosmic_public = fields.ListField(required=False, items_types=(CosmicPublic, ), help_text="Cosmic")
+    sanger_cosmic_licensed = fields.ListField(required=False, items_types=(CosmicLicensed, ), help_text="Cosmic")
+    ncbi_clinvar = fields.ListField(required=False, items_types=(ClinVar, ), help_text="ClinVar")
+    ncbi_clinvar2 = fields.ListField(required=False, items_types=(ClinVar2, ), help_text="ClinVar2")
+    icgc_somatic = fields.ListField(required=False, items_types=(Somatic, ), help_text="ICGC Somatic")
+    iarc_tp53_germline = fields.ListField(required=False, items_types=(TP53Germline, ), help_text="IARC TP53 Germline")
+    iarc_tp53_somatic = fields.ListField(required=False, items_types=(TP53Somatic, ), help_text="IARC TP53 Somatic")
+    pub_med_articles = DictField(required=False, help_text="PUBMED Articles")
+    uniprot_variants = fields.ListField(required=False, items_types=(UniprotVariants, ), help_text="UniProt variants")
+    wustl_civic = fields.ListField(required=False, items_types=(Civic, ), help_text="CIViC")
+    gwas = fields.ListField(required=False, items_types=(GWAS, ), help_text="GWAS")
+
+
+    @property
+    def genes(self):
+        genes = []
+        for transcript in self.refseq_transcripts:
+            for item in transcript.items:
+                if item.gene_symbol:
+                    genes.append(item.gene_symbol)
+        return genes
\ No newline at end of file
diff --git a/variantapi/vcf.py b/variantapi/vcf.py
new file mode 100644
index 0000000..ecd8e68
--- /dev/null
+++ b/variantapi/vcf.py
@@ -0,0 +1,52 @@
+from collections import OrderedDict
+
+from variantapi.client import VariantAPIClient, VariantApiException
+import os, vcf
+
+from variantapi.models.variant import AnnotatedVariant
+
+__author__ = "ckopanos"
+
+
+class VCFAnnotator(VariantAPIClient):
+    """
+    VCFAnnotator will take an input vcf file parse it and produce an annotated vcf file
+    """
+
+    def __init__(self, api_key=None,
+                 max_variants_per_batch=200, ref_genome='hg19', get_parametes=None):
+        super().__init__(api_key, max_variants_per_batch)
+        self.ref_genome = ref_genome
+        self.get_parameters = get_parametes
+
+    def annotate(self, input_vcf_file, output_vcf_file=None):
+        if not os.path.isfile(input_vcf_file):
+            raise FileNotFoundError('%s does not exist' % input_vcf_file)
+        if output_vcf_file is None:
+            output_vcf_file = "%s.annotated.vcf" % input_vcf_file
+        vcf_reader = vcf.Reader(filename=input_vcf_file)
+        vcf_writer = vcf.Writer(open(output_vcf_file, 'w'), vcf_reader)
+        input_batch = OrderedDict()
+        for record in vcf_reader:
+            for alt_seq in record.ALT:
+                requested_variant = "%s:%s:%s:%s" % (record.CHROM, record.POS, record.REF or "", alt_seq or "")
+                input_batch[requested_variant] = record
+            if len(input_batch) < self.max_variants_per_batch:
+                continue
+            api_results = self.batch_lookup(list(input_batch.keys()), params=self.get_parameters, ref_genome=self.ref_genome)
+            for i, requested_variant in enumerate(input_batch.keys()):
+                try:
+                    variant_result = AnnotatedVariant(**api_results[i])
+                    record = input_batch[requested_variant]
+                    record.INFO['VARIANT_ID'] = variant_result.variant_id
+                    record.INFO['GENE'] = ",".join(variant_result.genes)
+                except Exception as e:
+                    print(api_results[i]['variant_id'], e)
+                    pass
+                vcf_writer.write_record(record)
+
+
+            # reset input batch
+            input_batch = OrderedDict()
+
+

From da01bece26d0a280736b3d3f3a9049b2646de29b Mon Sep 17 00:00:00 2001
From: Richard Meyer <Richard.Meyer@saphetor.com>
Date: Wed, 13 Dec 2017 10:23:20 +0000
Subject: [PATCH 02/31] API-106 Changed file permissions + tweaked the README
 file.

---
 README.md                                     | 21 ++++++++++++++++++-
 batchRequestClient.py                         |  0
 setup.py                                      |  0
 variantapi/__init__.py                        |  0
 variantapi/client.py                          |  0
 variantapi/models/__init__.py                 |  0
 variantapi/models/elements/__init__.py        |  0
 variantapi/models/elements/broad.py           |  0
 variantapi/models/elements/dann.py            |  0
 variantapi/models/elements/dbnsfp.py          |  0
 variantapi/models/elements/gerp.py            |  0
 variantapi/models/elements/gnomad.py          |  0
 variantapi/models/elements/gwas.py            |  0
 variantapi/models/elements/iarc.py            |  0
 variantapi/models/elements/icgc.py            |  0
 variantapi/models/elements/isb.py             |  0
 variantapi/models/elements/ncbi.py            |  0
 variantapi/models/elements/sanger.py          |  0
 .../models/elements/thousand_genomes.py       |  0
 variantapi/models/elements/transcript.py      |  0
 variantapi/models/elements/uniprot.py         |  0
 variantapi/models/elements/wustl.py           |  0
 variantapi/models/fields.py                   |  0
 variantapi/models/variant.py                  |  0
 variantapi/vcf.py                             |  0
 25 files changed, 20 insertions(+), 1 deletion(-)
 mode change 100644 => 100755 batchRequestClient.py
 mode change 100644 => 100755 setup.py
 mode change 100644 => 100755 variantapi/__init__.py
 mode change 100644 => 100755 variantapi/client.py
 mode change 100644 => 100755 variantapi/models/__init__.py
 mode change 100644 => 100755 variantapi/models/elements/__init__.py
 mode change 100644 => 100755 variantapi/models/elements/broad.py
 mode change 100644 => 100755 variantapi/models/elements/dann.py
 mode change 100644 => 100755 variantapi/models/elements/dbnsfp.py
 mode change 100644 => 100755 variantapi/models/elements/gerp.py
 mode change 100644 => 100755 variantapi/models/elements/gnomad.py
 mode change 100644 => 100755 variantapi/models/elements/gwas.py
 mode change 100644 => 100755 variantapi/models/elements/iarc.py
 mode change 100644 => 100755 variantapi/models/elements/icgc.py
 mode change 100644 => 100755 variantapi/models/elements/isb.py
 mode change 100644 => 100755 variantapi/models/elements/ncbi.py
 mode change 100644 => 100755 variantapi/models/elements/sanger.py
 mode change 100644 => 100755 variantapi/models/elements/thousand_genomes.py
 mode change 100644 => 100755 variantapi/models/elements/transcript.py
 mode change 100644 => 100755 variantapi/models/elements/uniprot.py
 mode change 100644 => 100755 variantapi/models/elements/wustl.py
 mode change 100644 => 100755 variantapi/models/fields.py
 mode change 100644 => 100755 variantapi/models/variant.py
 mode change 100644 => 100755 variantapi/vcf.py

diff --git a/README.md b/README.md
index 35e2ed9..fb95b2e 100644
--- a/README.md
+++ b/README.md
@@ -11,6 +11,25 @@ within your code, or do
 
     pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
 
+Installation on Linux:
+...
+
+Installation on Mac OSX:
+- install pip using "sudo easy_install pip".
+- install the require Python libraries:  sudo pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
+
+Installation on Windows:
+...
+
+### Test run
+
+Try the following query to annotate a single variant:
+./run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
+
+The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensemble_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
+
+You are now ready to write your own code using the VarSome API.
+
 ### API Documentation
 
 Please visit the [api documentation](http://docs.varsome.apiary.io) to find out how to use the api and
@@ -21,7 +40,7 @@ what values does the api provide as a response to lookup requests
 You generally are not required to have an api key to use the api, though the number of requests you will be able
 to issue will be throttled if they exceed a certain number.
 
-Without an API key you will not be able to perform batch requests as well.
+An API key is required in order to batch requests or enable allele frequency filtering.
 
 To obtain an API key please [contact us](mailto:support@saphetor.com)
 
diff --git a/batchRequestClient.py b/batchRequestClient.py
old mode 100644
new mode 100755
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755
diff --git a/variantapi/__init__.py b/variantapi/__init__.py
old mode 100644
new mode 100755
diff --git a/variantapi/client.py b/variantapi/client.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/__init__.py b/variantapi/models/__init__.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/__init__.py b/variantapi/models/elements/__init__.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/broad.py b/variantapi/models/elements/broad.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/dann.py b/variantapi/models/elements/dann.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/dbnsfp.py b/variantapi/models/elements/dbnsfp.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/gerp.py b/variantapi/models/elements/gerp.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/gnomad.py b/variantapi/models/elements/gnomad.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/gwas.py b/variantapi/models/elements/gwas.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/iarc.py b/variantapi/models/elements/iarc.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/icgc.py b/variantapi/models/elements/icgc.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/isb.py b/variantapi/models/elements/isb.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/ncbi.py b/variantapi/models/elements/ncbi.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/sanger.py b/variantapi/models/elements/sanger.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/thousand_genomes.py b/variantapi/models/elements/thousand_genomes.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/transcript.py b/variantapi/models/elements/transcript.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/uniprot.py b/variantapi/models/elements/uniprot.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/elements/wustl.py b/variantapi/models/elements/wustl.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/fields.py b/variantapi/models/fields.py
old mode 100644
new mode 100755
diff --git a/variantapi/models/variant.py b/variantapi/models/variant.py
old mode 100644
new mode 100755
diff --git a/variantapi/vcf.py b/variantapi/vcf.py
old mode 100644
new mode 100755

From f944cec493acd66dd7a554a449a1b308c844006c Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 5 Jan 2018 09:07:20 +0200
Subject: [PATCH 03/31] Refactoring Work in progress. closes #3 closes #4

---
 annotate_vcf.py              |   28 +-
 batchRequestClient.py        |   85 --
 output.vcf                   | 2133 ----------------------------------
 run.py                       |   37 +-
 sample.vcf                   | 2132 ---------------------------------
 setup.py                     |    5 +-
 variantapi/client.py         |  113 +-
 variantapi/models/variant.py |   49 +-
 variantapi/vcf.py            |  116 +-
 9 files changed, 266 insertions(+), 4432 deletions(-)
 delete mode 100644 batchRequestClient.py
 delete mode 100644 output.vcf
 delete mode 100644 sample.vcf

diff --git a/annotate_vcf.py b/annotate_vcf.py
index b986173..e0fe770 100755
--- a/annotate_vcf.py
+++ b/annotate_vcf.py
@@ -1,39 +1,41 @@
 #!/usr/bin/env python
 import argparse
-import json
-import logging
 import sys
 
-from variantapi.client import VariantAPIClient
 from variantapi.vcf import VCFAnnotator
 
 __author__ = 'ckopanos'
-logging.basicConfig(level=logging.DEBUG,
-                    format='[%(levelname)s]	%(threadName)s	%(message)s',
-                    )
 
 
-def main(argv):
+def annotate_vcf(argv):
     parser = argparse.ArgumentParser(description='VCF Annotator command line')
     parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True)
     parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
                         required=False, default='hg19')
-    parser.add_argument('-f',
+    parser.add_argument('-i',
                         help='Path to vcf file',
-                        type=str, metavar='VCF File', required=True)
+                        type=str, metavar='Input VCF File', required=True)
+    parser.add_argument('-o',
+                        help='Path to output vcf file',
+                        type=str, metavar='Output VCF File', required=False)
     parser.add_argument('-p',
                         help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
                         type=str, metavar='Request Params', required=False, nargs='+')
+    parser.add_argument('-t', help='Run vcf annotator using x threads', type=int, default=3, required=False,
+                        metavar='Number of threads')
     args = parser.parse_args()
     api_key = args.k
-    vcf_file = args.f
+    vcf_file = args.i
+    output_vcf_file = args.o
     ref_genome = args.g
+    num_threads = args.t
     request_parameters = None
     if args.p:
         request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
-    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parametes=request_parameters)
-    vcf_annotator.annotate(vcf_file)
+    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parameters=request_parameters,
+                                 max_threads=num_threads)
+    vcf_annotator.annotate(vcf_file, output_vcf_file)
 
 
 if __name__ == "__main__":
-    main(sys.argv[1:])
+    annotate_vcf(sys.argv[1:])
diff --git a/batchRequestClient.py b/batchRequestClient.py
deleted file mode 100644
index 03f7fad..0000000
--- a/batchRequestClient.py
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env python3
-
-# A simple client application that does the following:
-# - Loads a text file containing one variant per row
-# - Performs a batch lookups to the Saphetor Variant API using N variants at a time. 
-# - Saves the results in a new file.
-#
-# It uses the following module:
-# variantapi.client (https://github.com/saphetor/variant-api-client-python)
-#
-# Note: To sort output json file execute:
-# jq -S '.' output.txt  > output_sorted.txt
-
-import argparse
-import json
-import logging
-import re
-import sys
-import operator
-from sys import argv
-from variantapi.client import VariantAPIClient
-
-__author__ = 'stephanos-androutsellis'
-
-# Declare reference genome as a global variable
-_ref_genome = 1019
-
-
-def main(argv):
-	# Read and parse arguments
-	infile = ''
-	outfile = ''
-	batch_size = 5000
-
-	parser = argparse.ArgumentParser(description='Simple batch lookup Client application')
-	parser.add_argument('-i', help='Input file', type=str, metavar='Input File', required=True)
-	parser.add_argument('-o', help='Output file', type=str, metavar='Output File', required=True)
-	parser.add_argument('-n', help="Number of variants to batch", type=int, metavar='Batch size', required=True,default=5000)
-	parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
-	parser.add_argument('-g', help='Reference genome either 1019 (default) or 1038', type=int, 
-		metavar='Reference Genome', required=False, default=1019)
-
-	args = parser.parse_args()
-	infile = args.i
-	outfile = args.o
-	batch_size = args.n if args.n is not None else batch_size
-	api_key = args.k
-	ref_genome = args.g if args.g is not None else _ref_genome
-
-	# Open and load input file into list
-	print("Reading input file ", infile)
-	with open(infile) as fi:
-		variants = fi.readlines()
-	variants = [v.strip('\n') for v in variants]
-
-	# Prepare output for writing.
-	print("Opening output file ", outfile)
-	fo = open(outfile,'w')
-
-	# Initialize client connection to API
-	api = VariantAPIClient(api_key)
-	if (api is None):
-		print("Failed to connect to API")
-		sys.exit()
-
-	batch_counter = 0
-	finished = False
-	while not finished:
-		start_index = batch_counter*batch_size
-		end_index = (batch_counter+1)*batch_size
-		if (end_index > len(variants)):
-			end_index = len(variants)
-			finished = True
-		print(start_index, ":", end_index-1)
-		batch_variants = variants[start_index:end_index]
-		print("Lookup for: ", batch_variants, "with ref_genome= ", ref_genome)
-		batch_data = api.batch_lookup(batch_variants, ref_genome=ref_genome)
-
-		fo.write(json.dumps(batch_data, indent=2))
-		batch_counter += 1
-
-	print ("Finished ", batch_counter, " batch lookups")
-
-if __name__ == '__main__':
-    main(argv)
diff --git a/output.vcf b/output.vcf
deleted file mode 100644
index eba086a..0000000
--- a/output.vcf
+++ /dev/null
@@ -1,2133 +0,0 @@
-##fileformat=VCFv4.1
-##GATKCommandLine=<ID=ApplyRecalibration,Version=3.3-0-g37228af,Date="Tue Jun 30 08:48:57 CEST 2015",Epoch=1435646937859,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ref/genomes/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=gatk/raw.variants.vcf)] recal_file=(RodBinding name=recal_file source=gatk/recalibrate_SNP.recal) tranches_file=gatk/recalibrate_SNP.tranches out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=ApplyRecalibration,Version=3.3-0-g37228af,Date="Tue Jun 30 08:49:46 CEST 2015",Epoch=1435646986265,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ref/genomes/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=gatk/recalibrated_snps_raw_indels.vcf)] recal_file=(RodBinding name=recal_file source=gatk/recalibrate_INDEL.recal) tranches_file=gatk/recalibrate_INDEL.tranches out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Tue Jun 30 02:53:50 CEST 2015",Epoch=1435625630685,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[bam/recalibrated.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ref/genomes/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name=dbsnp source=/ref/genomes/hg19/broad/dbsnp_138.hg19.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##reference=file:///ref/genomes/hg19/hg19.fa
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
-##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
-##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
-##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
-##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
-##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
-##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
-##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
-##INFO=<ID=GENE,Number=.,Type=String,Description="Concatenated list of GENE sumbols">
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.4085 <= x < 0.0794">
-##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -1678.3953">
-##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1678.3953 <= x < -2.4085">
-##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.501 <= x < 0.319">
-##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -1474.3646">
-##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1474.3646 <= x < -1.501">
-##contig=<ID=chrM,length=16571>
-##contig=<ID=chr1,length=249250621>
-##contig=<ID=chr2,length=243199373>
-##contig=<ID=chr3,length=198022430>
-##contig=<ID=chr4,length=191154276>
-##contig=<ID=chr5,length=180915260>
-##contig=<ID=chr6,length=171115067>
-##contig=<ID=chr7,length=159138663>
-##contig=<ID=chr8,length=146364022>
-##contig=<ID=chr9,length=141213431>
-##contig=<ID=chr10,length=135534747>
-##contig=<ID=chr11,length=135006516>
-##contig=<ID=chr12,length=133851895>
-##contig=<ID=chr13,length=115169878>
-##contig=<ID=chr14,length=107349540>
-##contig=<ID=chr15,length=102531392>
-##contig=<ID=chr16,length=90354753>
-##contig=<ID=chr17,length=81195210>
-##contig=<ID=chr18,length=78077248>
-##contig=<ID=chr19,length=59128983>
-##contig=<ID=chr20,length=63025520>
-##contig=<ID=chr21,length=48129895>
-##contig=<ID=chr22,length=51304566>
-##contig=<ID=chrX,length=155270560>
-##contig=<ID=chrY,length=59373566>
-##contig=<ID=chr1_gl000191_random,length=106433>
-##contig=<ID=chr1_gl000192_random,length=547496>
-##contig=<ID=chr4_ctg9_hap1,length=590426>
-##contig=<ID=chr4_gl000193_random,length=189789>
-##contig=<ID=chr4_gl000194_random,length=191469>
-##contig=<ID=chr6_apd_hap1,length=4622290>
-##contig=<ID=chr6_cox_hap2,length=4795371>
-##contig=<ID=chr6_dbb_hap3,length=4610396>
-##contig=<ID=chr6_mann_hap4,length=4683263>
-##contig=<ID=chr6_mcf_hap5,length=4833398>
-##contig=<ID=chr6_qbl_hap6,length=4611984>
-##contig=<ID=chr6_ssto_hap7,length=4928567>
-##contig=<ID=chr7_gl000195_random,length=182896>
-##contig=<ID=chr8_gl000196_random,length=38914>
-##contig=<ID=chr8_gl000197_random,length=37175>
-##contig=<ID=chr9_gl000198_random,length=90085>
-##contig=<ID=chr9_gl000199_random,length=169874>
-##contig=<ID=chr9_gl000200_random,length=187035>
-##contig=<ID=chr9_gl000201_random,length=36148>
-##contig=<ID=chr11_gl000202_random,length=40103>
-##contig=<ID=chr17_ctg5_hap1,length=1680828>
-##contig=<ID=chr17_gl000203_random,length=37498>
-##contig=<ID=chr17_gl000204_random,length=81310>
-##contig=<ID=chr17_gl000205_random,length=174588>
-##contig=<ID=chr17_gl000206_random,length=41001>
-##contig=<ID=chr18_gl000207_random,length=4262>
-##contig=<ID=chr19_gl000208_random,length=92689>
-##contig=<ID=chr19_gl000209_random,length=159169>
-##contig=<ID=chr21_gl000210_random,length=27682>
-##contig=<ID=chrUn_gl000211,length=166566>
-##contig=<ID=chrUn_gl000212,length=186858>
-##contig=<ID=chrUn_gl000213,length=164239>
-##contig=<ID=chrUn_gl000214,length=137718>
-##contig=<ID=chrUn_gl000215,length=172545>
-##contig=<ID=chrUn_gl000216,length=172294>
-##contig=<ID=chrUn_gl000217,length=172149>
-##contig=<ID=chrUn_gl000218,length=161147>
-##contig=<ID=chrUn_gl000219,length=179198>
-##contig=<ID=chrUn_gl000220,length=161802>
-##contig=<ID=chrUn_gl000221,length=155397>
-##contig=<ID=chrUn_gl000222,length=186861>
-##contig=<ID=chrUn_gl000223,length=180455>
-##contig=<ID=chrUn_gl000224,length=179693>
-##contig=<ID=chrUn_gl000225,length=211173>
-##contig=<ID=chrUn_gl000226,length=15008>
-##contig=<ID=chrUn_gl000227,length=128374>
-##contig=<ID=chrUn_gl000228,length=129120>
-##contig=<ID=chrUn_gl000229,length=19913>
-##contig=<ID=chrUn_gl000230,length=43691>
-##contig=<ID=chrUn_gl000231,length=27386>
-##contig=<ID=chrUn_gl000232,length=40652>
-##contig=<ID=chrUn_gl000233,length=45941>
-##contig=<ID=chrUn_gl000234,length=40531>
-##contig=<ID=chrUn_gl000235,length=34474>
-##contig=<ID=chrUn_gl000236,length=41934>
-##contig=<ID=chrUn_gl000237,length=45867>
-##contig=<ID=chrUn_gl000238,length=39939>
-##contig=<ID=chrUn_gl000239,length=33824>
-##contig=<ID=chrUn_gl000240,length=41933>
-##contig=<ID=chrUn_gl000241,length=42152>
-##contig=<ID=chrUn_gl000242,length=43523>
-##contig=<ID=chrUn_gl000243,length=43341>
-##contig=<ID=chrUn_gl000244,length=39929>
-##contig=<ID=chrUn_gl000245,length=36651>
-##contig=<ID=chrUn_gl000246,length=38154>
-##contig=<ID=chrUn_gl000247,length=36422>
-##contig=<ID=chrUn_gl000248,length=39786>
-##contig=<ID=chrUn_gl000249,length=38502>
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR309291
-chr6	44387517	rs6923521	C	G	184.84	PASS	AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.81;SOR=3.912;VQSLOD=6.47;culprit=FS;GENE=CDC5L	GT:AD:DP:GQ:PL	1/1:0,6:6:18:213,18,0
-chr6	44410746	rs61581947	GT	G	17.78	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=5.93;SOR=2.303;GENE=CDC5L	GT:AD:DP:GQ:PL	1/1:0,2:2:6:54,6,0
-chr6	44453701	rs60176543	G	A	15.65	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	44505655	rs9296442	G	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	44526440	rs991234	A	C	36.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.37;SOR=0.693;VQSLOD=7.54;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:64,6,0
-chr6	44532454	rs76750540	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44547060	rs67452991	C	T	102.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.51;SOR=0.693;VQSLOD=5.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:130,12,0
-chr6	44562107	rs491616	G	C	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:28:40,0,28
-chr6	44575012	rs636287	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44584484	rs634631	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44585311	rs648579	T	C	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.91;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	44586011	rs651831	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44586363	rs6913259	C	T	171.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=6.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:200,15,0
-chr6	44595393	rs1767788	C	T	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=9.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	44605066	rs6934182	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44605461	rs4714809	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44629576	rs4257850	A	G	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	44635852	rs4711794	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44640206	rs527082	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44775098	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44780682	rs622923	G	T	14.68	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.34;SOR=1.609;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	44780701	rs559322	C	T	15.65	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	44781313	rs5875893	G	GA	15.82	LowQual	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=3.95;SOR=2.303;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
-chr6	44797271	rs9369514	C	A	241.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.54;SOR=2.584;VQSLOD=6.76;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,7:7:21:270,21,0
-chr6	44825715	rs9395051	C	A	71.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=7.41;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	44834094	rs3846896	G	A	15.65	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	44840376	rs1293588	A	C	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.79;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	44888740	rs608941	C	T	94.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.87;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	44899632	rs679713	T	C	1144.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.54;SOR=6.666;VQSLOD=6.85;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,27:27:81:1173,81,0
-chr6	44900253	rs3799986	A	G	188.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.64;SOR=3.611;VQSLOD=6.39;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,5:5:15:217,15,0
-chr6	44903248	rs10948186	C	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.97;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	44921320	rs10948187	C	T	89.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=2.833;VQSLOD=8.75;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,3:3:9:117,9,0
-chr6	44921962	rs625782	T	C	65.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=2.833;VQSLOD=7.9;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,3:3:9:93,9,0
-chr6	44935341	rs636845	C	T	60.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=8.15;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	44952716	rs5875900	GT	G	29.71	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.85;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:66,6,0
-chr6	44972729	rs1159132	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44988149	rs1475534	C	T	529.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=14;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.74;SOR=5.421;VQSLOD=7.17;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,14:14:42:558,42,0
-chr6	45003928	rs4398713	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45020697	rs2149872	A	G	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.4;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	45066168	rs150556986	G	A	167.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.388;ClippingRankSum=0.194;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.194;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=-0.968;SOR=1.402;VQSLOD=5.5;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	0/1:8,6:14:99:196,0,294
-chr6	45073967	rs2396381	A	G	88.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.43;SOR=2.833;VQSLOD=8.42;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,3:3:9:116,9,0
-chr6	45090876	.	T	C	19.79	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=9.89;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:47,6,0
-chr6	45159414	rs11321900	TA	T	24.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.36;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	45163350	rs1748242	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45170121	rs1284955	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45175908	rs9381373	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45177025	rs2396425	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45192941	rs6911320	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45203918	rs6937317	T	C	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.23;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	45268574	rs111541141	T	TAAGAC	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.28;culprit=FS;GENE=SUPT3H	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	45360194	rs9395099	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45390962	rs11498196	C	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.55;culprit=FS;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	45444061	rs2677110	C	T	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=9.1;culprit=FS;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	45444083	rs35663521	G	GA	38.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=7.75;culprit=FS;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	45456564	rs12215249	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45486207	rs7771889	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45511541	rs10948238	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45519443	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45521733	rs1201807	C	T	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.89;culprit=FS;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	45521847	rs70996341	ATGTG	A	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.79;culprit=FS;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	45523928	rs675613	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45523947	rs5875926	G	GA	24.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.36;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	45564510	rs713270	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45609347	.	G	GT	22.73	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=11.36;SOR=0.693;GENE=RUNX2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:59,6,0
-chr6	45705659	rs829913	T	A	96.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	45733276	rs6942337	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45749983	rs9357491	A	G	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	45754997	rs1037281	A	C	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=9.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	45764956	rs11276783	ACAGGGCAGCT	A	98.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.75;SOR=2.833;VQSLOD=7.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	45769869	rs10948257	G	A	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=7.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	45792170	rs12197564	G	T	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	45808216	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45833836	rs142466444	TTTTC	T	85.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=17.15;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:43:123,0,43
-chr6	45847678	rs2396559	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45851886	rs1932042	C	T	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	45858548	rs71566550	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45870999	rs35735653	CAG	C	269.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.457;DB;DP=33;FS=4.212;MLEAC=1;MLEAF=0.5;MQ=59.43;MQ0=0;MQRankSum=-1.588;POSITIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=0.239;SOR=1.802;VQSLOD=2.22;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	0/1:22,9:31:99:307,0,882
-chr6	45888576	rs34155361	ATGC	A	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.66;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	45893031	rs6939554	C	T	35.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.87;SOR=0.693;VQSLOD=7.73;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:63,6,0
-chr6	45901916	rs9349337	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45909139	rs11421773	C	CG	234.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.08;SOR=2.833;VQSLOD=6.34;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,8:8:27:272,27,0
-chr6	45914028	rs3777582	A	T	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=13.72;SOR=1.609;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	45915413	rs1890368	C	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.11;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	45915504	rs1890369	A	C	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.66;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	45919719	rs3777587	A	G	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=6.51;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	45919758	rs3777588	G	A	120.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=24.16;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.26;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	0/1:1,4:5:27:149,0,27
-chr6	45921108	rs3777590	G	C	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.08;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	45922849	rs3734206	C	T	1890.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=48;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.58;SOR=6.316;VQSLOD=6.34;culprit=QD;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1919,141,0
-chr6	45923126	rs6909306	A	C	252.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.6;SOR=4.407;VQSLOD=6.96;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,8:8:24:281,24,0
-chr6	45965608	rs3777612	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45989366	rs1204338	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45994992	rs1547605	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46025834	rs1535110	T	G	23.58	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=7.86;SOR=0.693;GENE=CLIC5	GT:AD:DP:GQ:PL	1/1:0,2:2:7:51,7,0
-chr6	46047269	rs9381423	T	C	124.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.945;ClippingRankSum=0.453;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-1.586;POSITIVE_TRAIN_SITE;QD=7.8;ReadPosRankSum=1.586;SOR=0.223;VQSLOD=4.04;culprit=QD;GENE=CLIC5	GT:AD:DP:GQ:PL	0/1:11,5:16:99:153,0,375
-chr6	46047458	rs3734207	C	T	3075.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.19;ClippingRankSum=-0.231;DB;DP=213;FS=0.542;MLEAC=1;MLEAF=0.5;MQ=59.59;MQ0=0;MQRankSum=-1.583;POSITIVE_TRAIN_SITE;QD=14.44;ReadPosRankSum=0.457;SOR=0.754;VQSLOD=1.68;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	0/1:107,105:212:99:3104,0,3533
-chr6	46048000	rs1416165	T	C	2778.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.171;ClippingRankSum=0.218;DB;DP=172;FS=0.639;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.131;POSITIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=-1.044;SOR=0.794;VQSLOD=1.61;culprit=FS;GENE=CLIC5	GT:AD:DP:GQ:PL	0/1:74,98:172:99:2807,0,2169
-chr6	46107115	rs61381984	A	AT	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=4;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=3.01;ReadPosRankSum=0.736;SOR=2.225;GENE=ENPP4	GT:AD:DP:GQ:PL	0/1:1,2:3:20:49,0,20
-chr6	46107312	rs11752816	G	A	1890.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.79;ClippingRankSum=0.077;DB;DP=125;FS=3.508;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.58;POSITIVE_TRAIN_SITE;QD=15.13;ReadPosRankSum=-1.351;SOR=0.335;VQSLOD=2.14;culprit=ReadPosRankSum;GENE=ENPP4	GT:AD:DP:GQ:PL	0/1:62,63:125:99:1919,0,1762
-chr6	46107752	rs7451713	C	G	5119.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=7.032;ClippingRankSum=-2.826;DB;DP=301;FS=1.419;MLEAC=1;MLEAF=0.5;MQ=59.92;MQ0=0;MQRankSum=-0.805;POSITIVE_TRAIN_SITE;QD=17.01;ReadPosRankSum=0.708;SOR=0.792;VQSLOD=1.55;culprit=DP;GENE=ENPP4	GT:AD:DP:GQ:PL	0/1:146,155:301:99:5148,0,4240
-chr6	46110821	rs7769902	A	G	202.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.085;ClippingRankSum=0.38;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.78;MQ0=0;MQRankSum=-0.211;POSITIVE_TRAIN_SITE;QD=10.67;ReadPosRankSum=-0.549;SOR=0.321;VQSLOD=4.71;culprit=FS;GENE=ENPP4	GT:AD:DP:GQ:PL	0/1:12,7:19:99:231,0,378
-chr6	46110844	rs35942390	T	TGA	174.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.717;ClippingRankSum=-0.444;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.95;MQ0=0;MQRankSum=1.467;POSITIVE_TRAIN_SITE;QD=6.47;ReadPosRankSum=-0.853;SOR=0.307;VQSLOD=5.69;culprit=FS;GENE=ENPP4	GT:AD:DP:GQ:PL	0/1:14,8:22:99:212,0,429
-chr6	46124799	rs9367237	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46129345	rs2235881	G	A	4707.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=6.532;ClippingRankSum=-0.307;DB;DP=317;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.01;MQ0=0;MQRankSum=0.655;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=2.066;SOR=0.698;VQSLOD=1.89;culprit=FS;GENE=ENPP5	GT:AD:DP:GQ:PL	0/1:162,154:316:99:4736,0,4689
-chr6	46135489	rs6926570	T	C	3065.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=6.245;ClippingRankSum=0.018;DB;DP=187;FS=1.135;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=0.009;POSITIVE_TRAIN_SITE;QD=16.39;ReadPosRankSum=1.61;SOR=0.809;VQSLOD=2.66;culprit=DP;GENE=ENPP5	GT:AD:DP:GQ:PL	0/1:96,91:187:99:3094,0,2997
-chr6	46135984	rs3806995	G	T	1685.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.855;ClippingRankSum=-0.003;DB;DP=117;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=14.41;ReadPosRankSum=2.665;SOR=0.727;VQSLOD=4.05;culprit=FS;GENE=ENPP5	GT:AD:DP:GQ:PL	0/1:61,56:117:99:1714,0,1985
-chr6	46148778	rs34512199	AT	A	24.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	46170924	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46206776	rs55832349	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46219283	rs6910477	G	A	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.19;culprit=FS;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	46259017	rs11389800	G	GT	13.89	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;QD=4.63;SOR=2.303;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:50,6,0
-chr6	46293328	rs2277121	G	A	717.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=19;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=5.994;VQSLOD=6.73;culprit=FS;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,19:19:57:746,57,0
-chr6	46296710	rs6906742	C	T	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	46302975	rs60870663	T	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.4;culprit=FS;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46302987	rs58585138	A	G	46.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=7.24;culprit=FS;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	46312875	rs9367242	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46321514	.	T	C	20.78	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	46326865	.	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RCAN2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46456536	rs9349362	C	T	33.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.66;culprit=FS;GENE=RCAN2	GT:AD:DP:GQ:PL	0/1:1,2:3:34:62,0,34
-chr6	46462514	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46469927	rs59470467	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46470622	rs67200907	G	A	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	46479322	rs1609661	A	G	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	46490097	rs4714943	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46512200	.	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46521602	rs699939	C	A	599.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.64;ClippingRankSum=0.714;DB;DP=46;FS=1.296;MLEAC=1;MLEAF=0.5;MQ=59.5;MQ0=0;MQRankSum=-0.647;POSITIVE_TRAIN_SITE;QD=13.04;ReadPosRankSum=2.186;SOR=0.911;VQSLOD=2.11;culprit=ReadPosRankSum;GENE=CYP39A1	GT:AD:DP:GQ:PL	0/1:27,19:46:99:628,0,724
-chr6	46563817	rs7761731	A	T	3102.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.173;ClippingRankSum=-1.345;DB;DP=194;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.76;MQ0=0;MQRankSum=0.519;POSITIVE_TRAIN_SITE;QD=15.99;ReadPosRankSum=0.699;SOR=0.739;VQSLOD=2.35;culprit=FS;GENE=CYP39A1	GT:AD:DP:GQ:PL	0/1:90,104:194:99:3131,0,2802
-chr6	46607081	rs3085602	AT	A	645.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=20;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.29;SOR=6.091;VQSLOD=5.95;culprit=FS;GENE=CYP39A1	GT:AD:DP:GQ:PL	1/1:0,20:20:60:683,60,0
-chr6	46620252	rs12192544	C	G	5715.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.691;ClippingRankSum=0.485;DB;DP=440;FS=1.133;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-2.934;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.99;ReadPosRankSum=-0.818;SOR=0.805;VQSLOD=-0.9355;culprit=MQRankSum;GENE=CYP39A1,SLC25A27	GT:AD:DP:GQ:PL	0/1:239,200:439:99:5744,0,6851
-chr6	46623698	rs3757241	T	C	6720.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=183;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.06;SOR=0.822;VQSLOD=5.03;culprit=FS;GENE=SLC25A27	GT:AD:DP:GQ:PL	1/1:0,179:179:99:6749,538,0
-chr6	46625274	rs9381468	A	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.35;culprit=DP;GENE=SLC25A27	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	46626353	rs953062	A	G	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.6;culprit=FS;GENE=SLC25A27	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	46630068	rs9381469	G	A	907.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.991;ClippingRankSum=-0.318;DB;DP=68;FS=14.136;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.231;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=1.115;SOR=3.003;VQSLOD=1.21;culprit=FS;GENE=SLC25A27	GT:AD:DP:GQ:PL	0/1:40,28:68:99:936,0,1206
-chr6	46637908	rs200254015	A	C	76.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.158;ClippingRankSum=-1.074;DB;DP=72;FS=148.77;MLEAC=1;MLEAF=0.5;MQ=59.36;MQ0=0;MQRankSum=-0.756;QD=1.07;ReadPosRankSum=-5.463;SOR=5.781;VQSLOD=-47.45;culprit=FS;GENE=SLC25A27	GT:AD:DP:GQ:PL	0/1:55,17:72:99:105,0,1883
-chr6	46649231	rs7740677	C	T	6652.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=183;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.56;SOR=2.067;VQSLOD=5.55;culprit=FS;GENE=TDRD6	GT:AD:DP:GQ:PL	1/1:0,183:183:99:6681,550,0
-chr6	46657057	rs3799277	A	G	4300.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=112;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.78;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.29;SOR=1.35;VQSLOD=6.24;culprit=FS;GENE=TDRD6	GT:AD:DP:GQ:PL	1/1:0,111:111:99:4329,334,0
-chr6	46658905	rs9381472	C	G	2370.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.957;ClippingRankSum=-1.243;DB;DP=147;FS=3.996;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.165;POSITIVE_TRAIN_SITE;QD=16.13;ReadPosRankSum=0.979;SOR=1.036;VQSLOD=2.15;culprit=DP;GENE=TDRD6	GT:AD:DP:GQ:PL	0/1:77,70:147:99:2399,0,2735
-chr6	46661937	rs55724083	CT	C	307.76	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.021;ClippingRankSum=0.615;DB;DP=81;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.11;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=3.8;ReadPosRankSum=0.542;SOR=3.026;VQSLOD=5.76;culprit=FS;GENE=TDRD6	GT:AD:DP:GQ:PL	0/1:6,30:36:22:345,0,22
-chr6	46672205	.	TCTCTCTCTCTCA	T	62.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.219;ClippingRankSum=0.361;DP=48;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.85;MQ0=0;MQRankSum=-1.307;QD=1.31;ReadPosRankSum=2.219;SOR=0.892;VQSLOD=2.56;culprit=FS;GENE=TDRD6,PLA2G7	GT:AD:DP:GQ:PL	0/1:15,5:20:99:100,0,440
-chr6	46672452	rs148052037	TAATC	T	1973.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.65;ClippingRankSum=1.355;DB;DP=107;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.1;MQ0=0;MQRankSum=-2.444;POSITIVE_TRAIN_SITE;QD=18.45;ReadPosRankSum=-0.854;SOR=0.718;VQSLOD=3.96;culprit=FS;GENE=TDRD6,PLA2G7	GT:AD:DP:GQ:PL	0/1:51,52:103:99:2011,0,3030
-chr6	46672943	rs1051931	A	G	6548.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=172;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.43;SOR=1.172;VQSLOD=3.94;culprit=FS;GENE=PLA2G7	GT:AD:DP:GQ:PL	1/1:0,170:170:99:6577,511,0
-chr6	46676019	rs2216465	C	G	430.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.311;ClippingRankSum=0.241;DB;DP=29;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.548;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=-0.022;SOR=0.518;VQSLOD=5.37;culprit=FS;GENE=PLA2G7	GT:AD:DP:GQ:PL	0/1:16,13:29:99:459,0,615
-chr6	46682079	rs1362931	A	C	1919.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=50;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.23;SOR=7.864;VQSLOD=7.44;culprit=FS;GENE=PLA2G7	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1948,150,0
-chr6	46683978	rs41361844	T	TA	363.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.549;ClippingRankSum=1.214;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.33;MQ0=0;MQRankSum=-0.419;POSITIVE_TRAIN_SITE;QD=11.02;ReadPosRankSum=1.046;SOR=0.473;VQSLOD=6.0;culprit=FS;GENE=PLA2G7	GT:AD:DP:GQ:PL	0/1:17,13:30:99:401,0,436
-chr6	46684222	rs1805017	C	T	2595.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.964;ClippingRankSum=-0.355;DB;DP=171;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.76;MQ0=0;MQRankSum=1.275;POSITIVE_TRAIN_SITE;QD=15.18;ReadPosRankSum=0.601;SOR=0.648;VQSLOD=2.6;culprit=FS;GENE=PLA2G7	GT:AD:DP:GQ:PL	0/1:85,85:170:99:2624,0,2396
-chr6	46685286	rs6929105	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PLA2G7	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46689762	rs9472830	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PLA2G7	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46695144	.	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PLA2G7	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46714081	rs141667902	GTTCTCC	G	187.87	PASS	AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.03;MQ0=0;QD=31.31;SOR=1.022;VQSLOD=5.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:225,15,0
-chr6	46727772	rs6918050	G	C	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.87;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	46730039	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=27.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46761495	rs2274656	G	A	1258.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.705;ClippingRankSum=0.492;DB;DP=66;FS=11.133;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=19.07;ReadPosRankSum=0.794;SOR=0.077;VQSLOD=0.934;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:26,40:66:99:1287,0,859
-chr6	46766467	rs872018	G	C	826.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.434;ClippingRankSum=0.387;DB;DP=45;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.49;MQ0=0;MQRankSum=0.716;POSITIVE_TRAIN_SITE;QD=18.37;ReadPosRankSum=-3.462;SOR=1.681;VQSLOD=3.22;culprit=ReadPosRankSum;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:22,22:44:99:855,0,1647
-chr6	46766468	rs872019	G	C	826.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.555;ClippingRankSum=-0.67;DB;DP=46;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=-0.329;POSITIVE_TRAIN_SITE;QD=17.97;ReadPosRankSum=-2.986;SOR=1.609;VQSLOD=4.2;culprit=ReadPosRankSum;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:23,22:45:99:855,0,1647
-chr6	46775361	rs2894714	A	G	95.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.76;SOR=1.179;VQSLOD=6.48;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	46777377	rs1833460	T	C	2742.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.7;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.37;SOR=5.892;VQSLOD=6.63;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,78:78:99:2771,235,0
-chr6	46784183	rs9367257	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.03;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	46793175	rs6920863	G	A	976.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.347;ClippingRankSum=0.69;DB;DP=69;FS=2.675;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.762;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=-0.654;SOR=0.378;VQSLOD=3.19;culprit=ReadPosRankSum;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:35,34:69:99:1005,0,1233
-chr6	46794048	rs2297018	C	G	1559.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.778;ClippingRankSum=1.15;DB;DP=86;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.92;MQ0=0;MQRankSum=0.527;POSITIVE_TRAIN_SITE;QD=18.14;ReadPosRankSum=-0.821;SOR=0.791;VQSLOD=4.49;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:41,45:86:99:1588,0,1376
-chr6	46797329	rs2274657	G	A	1320.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.675;ClippingRankSum=0.827;DB;DP=98;FS=1.251;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=-0.371;POSITIVE_TRAIN_SITE;QD=13.48;ReadPosRankSum=0.307;SOR=0.399;VQSLOD=3.23;culprit=DP;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:53,45:98:99:1349,0,1847
-chr6	46797515	rs6903045	G	A	68.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.406;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.66;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:3,3:6:73:97,0,73
-chr6	46801071	rs2274658	G	T	2458.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.72;ClippingRankSum=0.231;DB;DP=169;FS=2.721;MLEAC=1;MLEAF=0.5;MQ=59.86;MQ0=0;MQRankSum=-0.436;POSITIVE_TRAIN_SITE;QD=14.55;ReadPosRankSum=2.14;SOR=0.917;VQSLOD=2.52;culprit=ReadPosRankSum;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:89,80:169:99:2487,0,2786
-chr6	46802172	.	ATATTTATT	A	98.25	PASS	AC=2;AF=1.0;AN=2;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.56;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	46802370	rs4714952	G	A	4383.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=119;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.22;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.86;SOR=1.198;VQSLOD=7.13;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,119:119:99:4412,357,0
-chr6	46802901	rs2297021	G	C	87.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.72;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.38;MQ0=0;MQRankSum=0.72;POSITIVE_TRAIN_SITE;QD=14.63;ReadPosRankSum=-0.72;SOR=0.368;VQSLOD=5.79;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:2,4:6:67:116,0,67
-chr6	46803018	rs2297020	A	T	292.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.746;ClippingRankSum=0.04;DB;DP=32;FS=3.467;MLEAC=1;MLEAF=0.5;MQ=58.35;MQ0=0;MQRankSum=0.913;POSITIVE_TRAIN_SITE;QD=9.15;ReadPosRankSum=-0.357;SOR=1.659;VQSLOD=2.47;culprit=QD;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:21,11:32:99:321,0,590
-chr6	46803102	rs2297019	A	G	273.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.297;ClippingRankSum=-1.681;DB;DP=23;FS=1.74;MLEAC=1;MLEAF=0.5;MQ=58.99;MQ0=0;MQRankSum=-1.484;POSITIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=-0.495;SOR=0.925;VQSLOD=2.16;culprit=MQRankSum;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:12,10:22:99:302,0,349
-chr6	46803345	rs12196017	G	A	98.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.55;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.07;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=14.11;ReadPosRankSum=1.754;SOR=0.941;VQSLOD=6.35;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:3,4:7:96:127,0,96
-chr6	46806766	rs115391170	G	A	1395.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.528;ClippingRankSum=0.481;DB;DP=95;FS=14.804;MLEAC=1;MLEAF=0.5;MQ=56.8;MQ0=0;MQRankSum=2.724;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=14.69;ReadPosRankSum=1.677;SOR=0.144;VQSLOD=-0.1508;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1424,0,1271
-chr6	46806802	rs143826629	G	A	1031.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.214;ClippingRankSum=0.523;DB;DP=71;FS=2.497;MLEAC=1;MLEAF=0.5;MQ=56.16;MQ0=0;MQRankSum=0.719;QD=14.53;ReadPosRankSum=-0.144;SOR=0.401;VQSLOD=1.61;culprit=DP;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:36,35:71:99:1060,0,1434
-chr6	46806809	rs1804211	C	T	1130.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.852;ClippingRankSum=0.535;DB;DP=71;FS=1.182;MLEAC=1;MLEAF=0.5;MQ=55.98;MQ0=0;MQRankSum=-0.121;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=1.122;SOR=0.995;VQSLOD=3.2;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:34,37:71:99:1159,0,1325
-chr6	46806939	rs17468190	G	T	181.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.38;ClippingRankSum=0.244;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=46.24;MQ0=0;MQRankSum=-1.977;POSITIVE_TRAIN_SITE;QD=12.98;ReadPosRankSum=0.689;SOR=1.022;VQSLOD=4.95;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	0/1:5,7:12:99:210,0,155
-chr6	46806948	rs150225810	G	GTTTGGGGCAGCT	230.82	PASS	AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.62;MQ0=0;QD=19.23;SOR=3.912;VQSLOD=4.37;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,6:6:17:268,17,0
-chr6	46807040	rs1059276	C	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.88;culprit=FS;GENE=MEP1A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46817550	rs6929917	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46817982	rs6458525	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.65;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46821191	.	A	G	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:1,2:3:28:40,0,28
-chr6	46822349	rs475991	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46823695	rs657340	G	A	1861.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=53;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.21;SOR=1.893;VQSLOD=6.39;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1890,156,0
-chr6	46823805	rs58687946	A	AG	1627.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=50;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.74;MQ0=0;QD=32.55;SOR=2.511;VQSLOD=4.68;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1665,138,0
-chr6	46824279	rs526123	A	G	176.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.248;ClippingRankSum=1.203;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.96;MQ0=0;MQRankSum=-1.683;POSITIVE_TRAIN_SITE;QD=19.64;ReadPosRankSum=-0.573;SOR=1.402;VQSLOD=5.29;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:3,6:9:92:205,0,92
-chr6	46824448	rs643409	A	G	2848.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=83;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=34.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.32;SOR=1.816;VQSLOD=7.31;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,83:83:99:2877,250,0
-chr6	46824798	rs521502	C	G	420.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=11;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=4.977;VQSLOD=6.96;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,11:11:33:449,33,0
-chr6	46825595	rs2281443	G	A	37.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=8.08;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:65,6,0
-chr6	46825632	rs627910	G	C	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.37;SOR=2.303;VQSLOD=7.74;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	46826508	rs613870	G	A	2427.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=67;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=0.917;VQSLOD=7.01;culprit=DP;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,67:67:99:2456,202,0
-chr6	46826715	rs572248	T	A	4133.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=118;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.35;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=0.881;VQSLOD=6.5;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,114:114:99:4162,343,0
-chr6	46826844	rs571247	T	C	5230.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=144;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.63;SOR=1.006;VQSLOD=6.93;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,144:144:99:5259,433,0
-chr6	46826910	rs611779	G	A	4855.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=132;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.04;SOR=1.119;VQSLOD=5.95;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,132:132:99:4884,397,0
-chr6	46826979	rs9381487	A	G	1623.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.727;ClippingRankSum=-0.199;DB;DP=106;FS=2.83;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-0.13;POSITIVE_TRAIN_SITE;QD=15.32;ReadPosRankSum=0.117;SOR=1.041;VQSLOD=2.59;culprit=DP;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:54,52:106:99:1652,0,1669
-chr6	46827073	rs547499	A	G	1003.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.612;ClippingRankSum=-0.887;DB;DP=64;FS=0.955;MLEAC=1;MLEAF=0.5;MQ=58.48;MQ0=0;MQRankSum=-0.699;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.094;SOR=0.831;VQSLOD=2.97;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:31,33:64:99:1032,0,968
-chr6	46827126	rs610856	C	T	2450.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=64;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.98;SOR=0.966;VQSLOD=5.61;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2479,192,0
-chr6	46827239	rs9395218	C	T	1247.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.769;ClippingRankSum=-0.087;DB;DP=83;FS=13.228;MLEAC=1;MLEAF=0.5;MQ=51.7;MQ0=0;MQRankSum=0.844;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=1.346;SOR=0.158;VQSLOD=1.45;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:39,44:83:99:1276,0,1186
-chr6	46828670	rs540727	A	G	1780.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=46;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.96;SOR=4.804;VQSLOD=6.53;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1809,138,0
-chr6	46830243	rs483813	T	C	95.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=8.22;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	46832536	rs531049	T	C	161.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.38;SOR=3.611;VQSLOD=6.6;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,5:5:15:190,15,0
-chr6	46832553	rs530990	A	G	80.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=2.833;VQSLOD=8.23;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:108,9,0
-chr6	46832642	rs615677	A	C	985.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=26;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.43;SOR=6.593;VQSLOD=7.43;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,26:26:78:1014,78,0
-chr6	46832741	rs529201	T	C	4511.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=123;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.57;SOR=3.352;VQSLOD=5.31;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,123:123:99:4540,368,0
-chr6	46832813	rs614826	G	A	3006.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.723;ClippingRankSum=-0.748;DB;DP=234;FS=8.321;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=1.246;POSITIVE_TRAIN_SITE;QD=12.85;ReadPosRankSum=1.65;SOR=1.157;VQSLOD=1.43;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:127,107:234:99:3035,0,4266
-chr6	46834473	rs586986	T	G	189.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.86;SOR=3.611;VQSLOD=5.55;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,5:5:15:218,15,0
-chr6	46834685	rs586024	G	A	4443.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=121;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.5;SOR=1.857;VQSLOD=6.18;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,121:121:99:4472,364,0
-chr6	46834906	rs5875987	TG	T	2501.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.68;SOR=3.007;VQSLOD=5.93;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2539,205,0
-chr6	46836406	rs665551	G	C	117.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.26;SOR=3.258;VQSLOD=5.89;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,4:4:12:145,12,0
-chr6	46836995	rs515866	T	C	146.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.38;SOR=3.611;VQSLOD=6.79;culprit=DP;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,5:5:15:175,15,0
-chr6	46839435	rs58989382	T	C	406.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.854;ClippingRankSum=-0.174;DB;DP=24;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.927;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=2.202;SOR=0.859;VQSLOD=4.91;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:11,13:24:99:435,0,357
-chr6	46841306	rs220675	T	C	195.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.97;SOR=0.941;VQSLOD=5.21;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,7:7:21:224,21,0
-chr6	46846277	rs220668	G	A	565.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=15;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.42;SOR=5.549;VQSLOD=6.31;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,15:15:45:594,45,0
-chr6	46847501	rs2273265	T	G	803.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.965;ClippingRankSum=0.7;DB;DP=55;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.735;POSITIVE_TRAIN_SITE;QD=14.61;ReadPosRankSum=1.889;SOR=1.223;VQSLOD=5.17;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:31,23:54:99:832,0,1017
-chr6	46849057	rs11760108	G	T	191.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.98;ClippingRankSum=0.068;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.75;MQ0=0;MQRankSum=0.299;POSITIVE_TRAIN_SITE;QD=12.78;ReadPosRankSum=0.201;SOR=0.693;VQSLOD=6.72;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:7,7:14:99:220,0,248
-chr6	46852193	rs220663	C	T	254.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.99;SOR=4.174;VQSLOD=7.14;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,7:7:21:283,21,0
-chr6	46855734	.	C	CAGGGAAGAGGACCCAGTAGTTTATCTGCCCA	53.7	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.93;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	46856100	rs678312	G	A	5756.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=152;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.73;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.1;SOR=1.091;VQSLOD=6.42;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,152:152:99:5785,457,0
-chr6	46858081	rs9472896	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=7.76;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	46867717	rs220702	C	T	2958.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.4;SOR=3.316;VQSLOD=6.24;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,78:78:99:2987,235,0
-chr6	46867898	rs3215601	TA	T	1316.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=41;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.26;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.12;SOR=5.892;VQSLOD=4.96;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1354,114,0
-chr6	46869895	rs220698	T	G	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.36;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	46874325	rs114267112	T	G	1871.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.381;ClippingRankSum=1.525;DB;DP=109;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.943;POSITIVE_TRAIN_SITE;QD=17.17;ReadPosRankSum=2.083;SOR=0.752;VQSLOD=2.72;culprit=MQRankSum;GENE=ADGRF5	GT:AD:DP:GQ:PL	0/1:53,56:109:99:1900,0,1690
-chr6	46895158	rs6458530	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.44;culprit=FS;GENE=ADGRF5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46928378	rs2396803	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46929606	rs1889578	T	C	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	46931019	rs4714972	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46932290	rs9472940	T	C	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:32:40,0,32
-chr6	46935422	rs9296519	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46980115	rs1226479	G	A	103.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.036;ClippingRankSum=0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=10.38;ReadPosRankSum=0.741;SOR=0.412;VQSLOD=6.3;culprit=FS;GENE=ADGRF1	GT:AD:DP:GQ:PL	0/1:6,4:10:99:132,0,220
-chr6	46986916	rs1226496	G	A	100.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.01;SOR=1.609;VQSLOD=8.14;culprit=FS;GENE=ADGRF1	GT:AD:DP:GQ:PL	1/1:0,4:4:12:128,12,0
-chr6	47015046	rs1352665	G	T	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	47029819	rs945217	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47037438	rs1226539	G	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	47079304	rs10948329	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47106677	.	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47116726	rs2003031	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=26.37;SOR=2.303;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	47163022	rs76480727	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47176242	rs11368956	C	CA	44.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	47200360	.	AAC	A	225.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.23;MQ0=0;MQRankSum=-0.751;QD=12.54;ReadPosRankSum=-0.751;SOR=3.056;VQSLOD=4.97;culprit=FS;GENE=TNFRSF21	GT:AD:DP:GQ:PL	0/1:1,11:12:4:212,0,4
-chr6	47200703	rs202137000	A	C	155.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.08;ClippingRankSum=0.291;DB;DP=89;FS=88.069;MLEAC=1;MLEAF=0.5;MQ=56.54;MQ0=0;MQRankSum=-0.508;QD=1.75;ReadPosRankSum=-1.601;SOR=6.868;VQSLOD=-14.2;culprit=FS;GENE=TNFRSF21	GT:AD:DP:GQ:PL	0/1:59,30:89:99:184,0,1744
-chr6	47228836	rs4715001	C	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.8;culprit=FS;GENE=TNFRSF21	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	47228912	rs10807350	G	A	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.68;culprit=FS;GENE=TNFRSF21	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	47369341	rs4301296	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47373447	rs1931826	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47425273	rs1889494	T	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	47450481	rs9395261	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47462615	rs2184398	T	C	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.42;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	47464881	rs62410680	G	A	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=23.04;SOR=2.833;VQSLOD=7.19;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	47464883	rs202187543	G	GT	98.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.88;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	47467043	rs34508069	A	ATG	34.71	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=0.693;VQSLOD=7.53;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
-chr6	47470146	rs1564926	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47489866	rs62410686	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47494842	rs35617629	T	TC	24.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=8.24;SOR=0.693;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	47512229	rs6915993	C	T	472.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.902;ClippingRankSum=-1.52;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.645;POSITIVE_TRAIN_SITE;QD=16.88;ReadPosRankSum=-0.369;SOR=0.836;VQSLOD=5.04;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:13,15:28:99:501,0,447
-chr6	47512590	rs6916578	C	T	344.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.172;ClippingRankSum=-0.793;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.34;POSITIVE_TRAIN_SITE;QD=21.55;ReadPosRankSum=-0.566;SOR=1.609;VQSLOD=6.22;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:5,11:16:99:373,0,169
-chr6	47522357	rs9473132	G	A	2114.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.279;ClippingRankSum=0.098;DB;DP=140;FS=1.431;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.117;POSITIVE_TRAIN_SITE;QD=15.11;ReadPosRankSum=-0.616;SOR=0.874;VQSLOD=2.05;culprit=DP;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:66,74:140:99:2143,0,2115
-chr6	47530422	rs9395277	A	C	559.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.99;SOR=5.549;VQSLOD=6.68;culprit=QD;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,15:15:45:588,45,0
-chr6	47532683	rs9395278	T	A	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.0;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	47545058	rs978448	C	T	76.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.988;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.6;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:3,3:6:99:105,0,105
-chr6	47548672	rs1014001	C	A	2124.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.361;ClippingRankSum=1.15;DB;DP=186;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=1.434;POSITIVE_TRAIN_SITE;QD=11.42;ReadPosRankSum=-1.001;SOR=0.701;VQSLOD=1.41;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:112,73:185:99:2153,0,3635
-chr6	47549586	rs6926592	A	T	31.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.47;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=3.53;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.09;culprit=QD;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:2,2:4:60:60,0,65
-chr6	47549883	rs2275446	T	C	1040.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.815;ClippingRankSum=-1.023;DB;DP=59;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.902;POSITIVE_TRAIN_SITE;QD=17.64;ReadPosRankSum=1.327;SOR=1.609;VQSLOD=5.52;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:30,29:59:99:1069,0,967
-chr6	47563692	rs2039503	C	T	15612.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=434;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.93;MQ0=0;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.86;SOR=1.288;VQSLOD=0.729;culprit=DP;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,433:433:99:15641,1302,0
-chr6	47577064	rs9395287	G	A	1930.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.08;ClippingRankSum=-0.414;DB;DP=155;FS=5.202;MLEAC=1;MLEAF=0.5;MQ=59.55;MQ0=0;MQRankSum=1.011;POSITIVE_TRAIN_SITE;QD=12.46;ReadPosRankSum=1.551;SOR=0.345;VQSLOD=2.02;culprit=DP;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:89,66:155:99:1959,0,2911
-chr6	47591856	rs10948368	T	C	837.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.469;ClippingRankSum=1.334;DB;DP=42;FS=3.025;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.826;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=1.309;SOR=0.151;VQSLOD=2.32;culprit=QD;GENE=CD2AP	GT:AD:DP:GQ:PL	0/1:18,24:42:99:866,0,595
-chr6	47592328	rs11309569	GT	G	75.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.27;culprit=FS;GENE=CD2AP	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	47611404	rs13196954	C	G	36.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.937;ClippingRankSum=0.0;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=5.25;ReadPosRankSum=0.937;SOR=0.446;VQSLOD=4.88;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,3:7:65:65,0,111
-chr6	47611442	rs7766527	T	C	84.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-0.421;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-2.017;POSITIVE_TRAIN_SITE;QD=10.6;ReadPosRankSum=0.421;SOR=1.609;VQSLOD=4.55;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:113,0,102
-chr6	47624115	rs1485782	C	T	140.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=20.11;ReadPosRankSum=1.495;SOR=1.609;VQSLOD=5.61;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:2,5:7:57:169,0,57
-chr6	47624129	rs1485783	G	A	221.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.65;MQ0=0;MQRankSum=-0.48;POSITIVE_TRAIN_SITE;QD=22.18;ReadPosRankSum=0.48;SOR=2.303;VQSLOD=5.41;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:2,8:10:57:250,0,57
-chr6	47624239	rs1485784	A	G	779.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.26;ClippingRankSum=-1.087;DB;DP=42;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=-0.455;POSITIVE_TRAIN_SITE;QD=18.57;ReadPosRankSum=-1.744;SOR=0.286;VQSLOD=5.1;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:19,23:42:99:808,0,614
-chr6	47624299	rs9369730	A	G	990.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.981;ClippingRankSum=0.405;DB;DP=68;FS=2.459;MLEAC=1;MLEAF=0.5;MQ=56.52;MQ0=0;MQRankSum=-0.459;POSITIVE_TRAIN_SITE;QD=14.57;ReadPosRankSum=2.549;SOR=0.389;VQSLOD=2.9;culprit=ReadPosRankSum;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:29,35:64:99:1019,0,894
-chr6	47624633	rs1021231	G	A	201.84	PASS	AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.04;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.64;SOR=3.912;VQSLOD=7.41;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	1/1:0,6:6:18:230,18,0
-chr6	47626149	rs6934553	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ADGRF2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47626490	rs10456129	G	C	47.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=15.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.4;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:1,2:3:30:76,0,30
-chr6	47626685	rs6935668	C	T	505.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.678;ClippingRankSum=-0.091;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.677;POSITIVE_TRAIN_SITE;QD=10.12;ReadPosRankSum=-0.677;SOR=0.67;VQSLOD=4.29;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:32,18:50:99:534,0,1085
-chr6	47626833	rs12201065	C	A	1126.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.697;ClippingRankSum=-0.211;DB;DP=79;FS=1.842;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.624;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=2.098;SOR=0.509;VQSLOD=3.19;culprit=ReadPosRankSum;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:42,37:79:99:1155,0,1430
-chr6	47631622	rs2396829	G	T	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609;GENE=ADGRF2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	47641307	rs1411049	G	C	1221.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.168;ClippingRankSum=0.23;DB;DP=74;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.479;POSITIVE_TRAIN_SITE;QD=16.51;ReadPosRankSum=-0.34;SOR=1.061;VQSLOD=4.74;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:31,43:74:99:1250,0,1019
-chr6	47645772	rs9369734	G	T	131.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.387;ClippingRankSum=-0.717;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.87;MQ0=0;MQRankSum=1.186;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=1.031;SOR=0.551;VQSLOD=4.95;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:6,5:11:99:160,0,198
-chr6	47646468	rs6929227	T	C	36.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.87;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:1,2:3:33:65,0,33
-chr6	47646842	rs6907125	A	G	1474.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.856;ClippingRankSum=0.375;DB;DP=112;FS=1.527;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=-0.67;POSITIVE_TRAIN_SITE;QD=13.17;ReadPosRankSum=-0.351;SOR=0.896;VQSLOD=2.99;culprit=DP;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:57,54:111:99:1503,0,1770
-chr6	47647004	rs6911739	C	T	236.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.835;ClippingRankSum=-0.289;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.536;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=0.289;SOR=0.495;VQSLOD=6.19;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:4,8:12:99:265,0,101
-chr6	47647593	rs58870329	GA	G	32.74	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.91;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.02;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:1,2:3:30:70,0,30
-chr6	47649222	rs8180544	T	G	3766.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.617;ClippingRankSum=-0.635;DB;DP=262;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-0.348;POSITIVE_TRAIN_SITE;QD=14.38;ReadPosRankSum=1.474;SOR=0.706;VQSLOD=1.98;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:130,131:261:99:3795,0,4054
-chr6	47649265	rs17541107	T	A	4039.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.52;ClippingRankSum=0.331;DB;DP=283;FS=5.506;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=-0.377;POSITIVE_TRAIN_SITE;QD=14.27;ReadPosRankSum=1.57;SOR=0.994;VQSLOD=1.83;culprit=DP;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:148,135:283:99:4068,0,4356
-chr6	47649573	rs10807371	C	T	3884.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.363;ClippingRankSum=0.166;DB;DP=210;FS=0.513;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=18.5;ReadPosRankSum=2.787;SOR=0.633;VQSLOD=1.64;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:110,99:209:99:3913,0,7372
-chr6	47649574	rs10807372	A	G	3884.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.254;ClippingRankSum=0.771;DB;DP=211;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=18.41;ReadPosRankSum=2.423;SOR=0.713;VQSLOD=1.59;culprit=FS;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:108,102:210:99:3913,0,7372
-chr6	47649694	rs9381594	A	G	2384.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.217;ClippingRankSum=0.797;DB;DP=160;FS=5.307;MLEAC=1;MLEAF=0.5;MQ=59.71;MQ0=0;MQRankSum=0.869;POSITIVE_TRAIN_SITE;QD=14.9;ReadPosRankSum=0.046;SOR=1.179;VQSLOD=2.22;culprit=DP;GENE=ADGRF2	GT:AD:DP:GQ:PL	0/1:82,78:160:99:2413,0,2636
-chr6	47653485	rs9369736	A	G	580.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.376;ClippingRankSum=-0.637;DB;DP=39;FS=6.87;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.099;POSITIVE_TRAIN_SITE;QD=14.89;ReadPosRankSum=1.119;SOR=2.2;VQSLOD=2.66;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:22,17:39:99:609,0,665
-chr6	47653536	rs9381596	A	G	676.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.398;ClippingRankSum=-1.699;DB;DP=50;FS=5.655;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.621;POSITIVE_TRAIN_SITE;QD=13.54;ReadPosRankSum=1.097;SOR=1.197;VQSLOD=1.88;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:26,24:50:99:705,0,787
-chr6	47654591	rs10948376	G	T	642.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.972;ClippingRankSum=-0.822;DB;DP=39;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.782;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=-0.752;SOR=1.085;VQSLOD=3.73;culprit=MQRankSum;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:14,20:34:99:671,0,497
-chr6	47654662	rs10485315	A	G	2893.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=7.315;ClippingRankSum=0.398;DB;DP=167;FS=1.004;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=17.33;ReadPosRankSum=2.188;SOR=0.957;VQSLOD=2.61;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:84,83:167:99:2922,0,2748
-chr6	47654742	rs9296573	A	T	4359.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.866;ClippingRankSum=0.983;DB;DP=296;FS=5.331;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=0.493;POSITIVE_TRAIN_SITE;QD=14.73;ReadPosRankSum=-1.261;SOR=0.468;VQSLOD=1.31;culprit=DP;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:143,153:296:99:4388,0,4431
-chr6	47654817	rs1556133	C	A	3193.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.266;ClippingRankSum=-0.767;DB;DP=141;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.607;POSITIVE_TRAIN_SITE;QD=22.65;ReadPosRankSum=0.439;SOR=0.716;VQSLOD=2.57;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:57,84:141:99:3222,0,2060
-chr6	47654831	rs1556132	A	G	3144.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.124;ClippingRankSum=-0.737;DB;DP=121;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.55;POSITIVE_TRAIN_SITE;QD=25.99;ReadPosRankSum=0.045;SOR=0.73;VQSLOD=2.91;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:47,74:121:99:3173,0,1780
-chr6	47654864	rs1556131	T	G	1356.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.916;ClippingRankSum=1.761;DB;DP=69;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.023;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.03;SOR=0.98;VQSLOD=4.41;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:30,39:69:99:1385,0,976
-chr6	47661115	rs6901702	T	C	90.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=2.833;VQSLOD=7.91;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:118,9,0
-chr6	47661248	rs36010404	AG	A	335.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.98;SOR=4.977;VQSLOD=6.17;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	1/1:0,11:11:33:373,33,0
-chr6	47661260	rs200900695	AC	A	126.76	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.589;ClippingRankSum=-0.354;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.65;MQ0=0;MQRankSum=-1.768;POSITIVE_TRAIN_SITE;QD=7.92;ReadPosRankSum=1.061;SOR=2.494;VQSLOD=4.52;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:2,9:11:22:164,0,22
-chr6	47661387	rs9395311	A	G	2320.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.015;ClippingRankSum=-0.577;DB;DP=139;FS=8.901;MLEAC=1;MLEAF=0.5;MQ=59.67;MQ0=0;MQRankSum=-0.615;POSITIVE_TRAIN_SITE;QD=16.7;ReadPosRankSum=2.635;SOR=0.237;VQSLOD=1.11;culprit=FS;GENE=ADGRF4,ADGRF2	GT:AD:DP:GQ:PL	0/1:64,75:139:99:2349,0,1921
-chr6	47675922	rs16876334	C	T	1527.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.988;ClippingRankSum=-0.373;DB;DP=82;FS=4.427;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.181;POSITIVE_TRAIN_SITE;QD=18.63;ReadPosRankSum=0.624;SOR=1.413;VQSLOD=1.23;culprit=MQRankSum;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:37,45:82:99:1556,0,1063
-chr6	47676150	rs9369737	C	T	269.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.291;ClippingRankSum=1.732;DB;DP=23;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.283;POSITIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=-0.346;SOR=0.368;VQSLOD=5.18;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:14,9:23:99:298,0,504
-chr6	47678455	rs11356177	CT	C	1687.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.012;ClippingRankSum=-0.222;DB;DP=162;FS=0.656;MLEAC=1;MLEAF=0.5;MQ=60.33;MQ0=0;MQRankSum=1.477;POSITIVE_TRAIN_SITE;QD=10.42;ReadPosRankSum=0.632;SOR=0.809;VQSLOD=1.77;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:80,76:156:99:1725,0,2007
-chr6	47678678	rs944056	C	G	3493.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=91;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.59;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.34;SOR=2.758;VQSLOD=7.4;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3522,271,0
-chr6	47678718	rs1318391	C	G	857.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.618;ClippingRankSum=0.693;DB;DP=61;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.08;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.97;SOR=0.439;VQSLOD=5.75;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:35,26:61:99:886,0,1329
-chr6	47678848	rs199503700	CAA	C	43.74	PASS	AC=1;AF=0.5;AN=2;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.87;SOR=2.303;VQSLOD=8.58;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:0,2:2:25:81,0,25
-chr6	47678861	rs9381602	A	G	52.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.93;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:1,2:3:25:81,0,25
-chr6	47680450	rs871654	A	C	516.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.618;ClippingRankSum=-0.634;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.41;POSITIVE_TRAIN_SITE;QD=24.61;ReadPosRankSum=0.634;SOR=1.508;VQSLOD=5.59;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:7,14:21:99:545,0,211
-chr6	47681494	rs6916562	T	C	3414.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=86;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.92;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.9;SOR=5.235;VQSLOD=6.11;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3443,259,0
-chr6	47682604	rs9369738	A	C	6287.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=181;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.74;SOR=1.468;VQSLOD=6.07;culprit=QD;GENE=ADGRF4,RN7SKP116	GT:AD:DP:GQ:PL	1/1:0,179:179:99:6316,538,0
-chr6	47682949	rs16876369	C	T	1708.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.057;ClippingRankSum=-0.481;DB;DP=110;FS=7.189;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.072;POSITIVE_TRAIN_SITE;QD=15.53;ReadPosRankSum=0.146;SOR=1.458;VQSLOD=1.58;culprit=FS;GENE=ADGRF4,RN7SKP116	GT:AD:DP:GQ:PL	0/1:54,56:110:99:1737,0,1465
-chr6	47683057	rs41452951	A	G	376.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.298;ClippingRankSum=-0.209;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.17;MQ0=0;MQRankSum=0.07;POSITIVE_TRAIN_SITE;QD=13.46;ReadPosRankSum=0.07;SOR=0.46;VQSLOD=5.39;culprit=FS;GENE=ADGRF4,RN7SKP116	GT:AD:DP:GQ:PL	0/1:16,12:28:99:405,0,546
-chr6	47684591	rs1360157	G	A	2096.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.035;ClippingRankSum=0.291;DB;DP=146;FS=1.305;MLEAC=1;MLEAF=0.5;MQ=59.71;MQ0=0;MQRankSum=0.615;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.971;SOR=0.572;VQSLOD=3.15;culprit=DP;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:74,71:145:99:2125,0,2159
-chr6	47686101	rs6914013	T	C	9061.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=255;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.19;SOR=1.281;VQSLOD=5.11;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	1/1:0,254:254:99:9090,763,0
-chr6	47686235	rs11754756	C	A	1895.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.892;ClippingRankSum=1.54;DB;DP=110;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.66;MQ0=0;MQRankSum=0.867;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.771;SOR=0.905;VQSLOD=3.88;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:50,60:110:99:1924,0,1695
-chr6	47686397	rs11476874	AT	A	63.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=-0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=62.13;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=12.75;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=6.6;culprit=FS;GENE=ADGRF4	GT:AD:DP:GQ:PL	0/1:2,3:5:66:101,0,66
-chr6	47690579	rs1329522	T	C	91.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.76;SOR=0.693;VQSLOD=6.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:119,12,0
-chr6	47690601	rs35597357	T	C	29.77	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=7.44;ReadPosRankSum=0.0;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:37:58,0,37
-chr6	47690613	rs1329523	G	A	81.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.179;VQSLOD=8.5;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:109,9,0
-chr6	47696780	rs2282337	C	T	36.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.38;ClippingRankSum=-0.72;DB;DP=6;FS=3.31;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=6.13;ReadPosRankSum=-0.72;SOR=2.303;VQSLOD=2.06;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,2:6:65:65,0,81
-chr6	47698280	rs1329540	G	A	94.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	47698303	rs1329539	C	T	94.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=7.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	47703969	rs949680	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47707247	rs72864549	C	T	37.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=6.9;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:65,6,0
-chr6	47708230	rs12199415	A	G	96.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	47708267	rs9473166	C	T	93.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=6.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	47712313	rs9349429	T	G	41.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.87;SOR=2.303;VQSLOD=8.76;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	47714073	rs9367302	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47720533	rs61744507	G	A	144.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.876;ClippingRankSum=-1.652;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.361;POSITIVE_TRAIN_SITE;QD=16.09;ReadPosRankSum=1.881;SOR=0.892;VQSLOD=5.73;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:173,0,134
-chr6	47720824	rs2039141	A	G	2982.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=82;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.6;SOR=1.697;VQSLOD=5.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3011,247,0
-chr6	47740398	rs1329529	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47746444	rs10485318	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47749539	rs9395320	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.35;culprit=FS;GENE=OPN5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	47749728	rs7741473	T	G	1371.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.498;ClippingRankSum=1.007;DB;DP=64;FS=3.91;MLEAC=1;MLEAF=0.5;MQ=58.91;MQ0=0;MQRankSum=0.168;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=-0.21;SOR=0.253;VQSLOD=2.29;culprit=QD;GENE=OPN5	GT:AD:DP:GQ:PL	0/1:23,41:64:99:1400,0,654
-chr6	47754498	rs1329543	A	G	352.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.647;ClippingRankSum=-0.208;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.052;POSITIVE_TRAIN_SITE;QD=13.57;ReadPosRankSum=0.052;SOR=0.446;VQSLOD=5.83;culprit=FS;GENE=OPN5	GT:AD:DP:GQ:PL	0/1:15,11:26:99:381,0,529
-chr6	47754538	rs6900985	T	C	166.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.859;ClippingRankSum=-1.156;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.653;POSITIVE_TRAIN_SITE;QD=9.81;ReadPosRankSum=0.653;SOR=0.293;VQSLOD=5.2;culprit=FS;GENE=OPN5	GT:AD:DP:GQ:PL	0/1:11,6:17:99:195,0,378
-chr6	47763514	rs139235050	TCACACA	T	98.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.1;MQ0=0;QD=19.65;SOR=2.833;VQSLOD=6.81;culprit=FS;GENE=OPN5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	47808012	rs474725	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47822105	rs532671	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47826378	rs476873	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47841953	rs4715047	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47845813	rs1887899	G	T	171.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=7.2;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,5:5:15:200,15,0
-chr6	47847179	rs3799276	A	G	11221.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=302;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.02;SOR=1.221;VQSLOD=2.8;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,301:301:99:11250,905,0
-chr6	47847401	rs2068006	A	G	6414.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=184;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.86;SOR=0.832;VQSLOD=4.02;culprit=QD;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,182:182:99:6443,547,0
-chr6	47847683	rs9367307	A	T	3379.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=142;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.8;SOR=3.095;VQSLOD=3.37;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,121:121:99:3408,364,0
-chr6	47862643	rs113155505	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47865882	rs4715053	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47869426	rs1360080	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.52;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	47869448	rs1360081	G	A	125.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.26;SOR=1.609;VQSLOD=7.95;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,4:4:12:153,12,0
-chr6	47871871	rs13194591	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.67;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	47871877	.	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	47927739	.	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47941339	rs2753188	G	A	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=6.28;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	47954722	rs2145363	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47977018	rs2753194	C	A	684.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.07;ClippingRankSum=1.38;DB;DP=36;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.36;MQ0=0;MQRankSum=0.995;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=1.508;SOR=1.061;VQSLOD=4.96;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	0/1:15,21:36:99:713,0,543
-chr6	47977136	rs45599036	C	T	79.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=19.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.45;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	0/1:1,3:4:26:108,0,26
-chr6	48005879	rs12205869	G	A	45.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=9.01;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	48009812	.	A	C	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PTCHD4	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	48015295	rs618543	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48015693	rs332554	A	G	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.12;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	48026377	rs647942	A	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.17;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	48032884	rs75735764	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48036051	rs201541883	A	C	779.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.322;ClippingRankSum=-0.178;DB;DP=120;FS=165.662;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-0.683;QD=6.5;ReadPosRankSum=-4.265;SOR=8.379;VQSLOD=-62.04;culprit=FS;GENE=PTCHD4	GT:AD:DP:GQ:PL	0/1:52,65:117:99:808,0,1315
-chr6	48083008	rs6908563	G	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	48117685	rs12523977	C	G	501.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.424;ClippingRankSum=0.073;DB;DP=38;FS=1.785;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.833;POSITIVE_TRAIN_SITE;QD=13.2;ReadPosRankSum=-2.675;SOR=1.329;VQSLOD=1.85;culprit=ReadPosRankSum;GENE=HNRNPA3P4	GT:AD:DP:GQ:PL	0/1:20,18:38:99:530,0,640
-chr6	48131753	rs1331118	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48172099	.	G	GGGA	46.7	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=23.35;SOR=0.693;VQSLOD=5.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	48195386	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48214766	rs2456916	A	G	38.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:33:67,0,33
-chr6	48214812	rs2503669	C	G	78.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.754;ClippingRankSum=0.937;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.55;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=11.25;ReadPosRankSum=1.3;SOR=2.775;VQSLOD=0.03;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,3:7:99:107,0,141
-chr6	48214977	rs2503670	A	G	44.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.19;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.4;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:71:73,0,71
-chr6	48215008	rs2496375	G	A	41.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=10.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.07;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:70:70,0,71
-chr6	48225108	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48262773	rs13202212	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48282517	rs11758955	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48282542	rs545090	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48396334	rs9473361	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48445933	rs1121646	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48448275	rs9473387	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48449928	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48450548	rs9784854	G	A	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=7.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	48456067	rs148792649	CAGTCTTGAAGACAAAATGCTAACATGTAATAAGAAAATATTTGA	C	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=7.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	48456290	rs7754822	G	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	48456315	rs9473391	A	T	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	48464593	rs9473403	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48467616	rs12206390	A	G	65.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=1.179;VQSLOD=8.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:93,9,0
-chr6	48468120	rs6915049	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48592097	.	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48596846	rs2912621	T	G	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	48609036	rs963049	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48615474	rs2433657	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48750072	rs2495881	T	C	75.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.09;SOR=2.833;VQSLOD=7.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:103,9,0
-chr6	48792612	rs2495863	C	T	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	48811854	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48825657	rs1938202	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48899692	rs10948458	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48919773	rs16878430	G	A	235.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.54;ClippingRankSum=-0.212;DB;DP=16;FS=4.467;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.318;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-1.059;SOR=0.525;VQSLOD=3.12;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:7,9:16:99:264,0,243
-chr6	48920376	rs12204534	C	T	96.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=2.833;VQSLOD=7.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	49011686	rs35984632	A	AT	50.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;QD=16.75;SOR=1.179;VQSLOD=7.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:87,9,0
-chr6	49022228	rs6458657	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49036510	rs12194577	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49045630	rs9367346	A	T	789.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.471;ClippingRankSum=-1.379;DB;DP=53;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.098;POSITIVE_TRAIN_SITE;QD=14.9;ReadPosRankSum=2.233;SOR=0.793;VQSLOD=5.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,26:53:99:818,0,792
-chr6	49052341	rs6458676	A	G	38.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=7.75;ReadPosRankSum=-0.358;SOR=1.179;VQSLOD=5.43;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,3:5:34:67,0,34
-chr6	49083404	.	A	G	43.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=10.94;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=3.54;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:61:72,0,61
-chr6	49169185	rs113197207	C	CTTCT	77.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.53;SOR=0.693;VQSLOD=8.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:9:114,9,0
-chr6	49199384	rs570913	T	G	15.65	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=15.65;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	49209747	rs9463466	G	T	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	49212193	rs492254	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49218084	rs7756663	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49218093	rs11453208	A	AT	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=6.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49397107	.	A	G	12.06	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:26:40,0,26
-chr6	49414272	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MUT	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49415351	.	TA	T	91.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.54;ClippingRankSum=-0.501;DP=115;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.85;MQ0=0;MQRankSum=0.642;POSITIVE_TRAIN_SITE;QD=0.8;ReadPosRankSum=0.146;SOR=0.653;VQSLOD=3.81;culprit=FS;GENE=MUT	GT:AD:DP:GQ:PL	0/1:57,17:74:99:129,0,1146
-chr6	49437853	rs11333073	AT	A	27.74	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.412;ClippingRankSum=-0.483;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.69;MQ0=0;MQRankSum=0.985;QD=0.55;ReadPosRankSum=0.77;SOR=0.976;GENE=CENPQ	GT:AD:DP:GQ:PL	0/1:38,8:46:65:65,0,808
-chr6	49456545	rs2501965	G	A	816.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=22;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.39;SOR=6.273;VQSLOD=4.58;culprit=FS;GENE=CENPQ	GT:AD:DP:GQ:PL	1/1:0,22:22:66:845,66,0
-chr6	49459978	rs2501968	A	G	4668.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=126;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.08;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.981;VQSLOD=6.45;culprit=FS;GENE=CENPQ	GT:AD:DP:GQ:PL	1/1:0,124:124:99:4697,373,0
-chr6	49460152	rs1471539	A	G	177.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.65;SOR=3.611;VQSLOD=5.84;culprit=FS;GENE=CENPQ	GT:AD:DP:GQ:PL	1/1:0,5:5:15:206,15,0
-chr6	49479750	rs13193063	T	C	340.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.4;SOR=1.445;VQSLOD=6.2;culprit=FS;GENE=GLYATL3	GT:AD:DP:GQ:PL	1/1:0,12:12:36:369,36,0
-chr6	49479775	rs1480615	A	T	224.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.11;SOR=2.584;VQSLOD=7.65;culprit=FS;GENE=GLYATL3	GT:AD:DP:GQ:PL	1/1:0,7:7:21:253,21,0
-chr6	49480339	rs9463493	A	G	64.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.26;culprit=FS;GENE=GLYATL3	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	49494241	rs9367359	A	G	3361.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=95;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.6;SOR=0.826;VQSLOD=7.14;culprit=FS;GENE=GLYATL3	GT:AD:DP:GQ:PL	1/1:0,94:94:99:3390,283,0
-chr6	49495862	rs6458696	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GLYATL3	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49497461	rs2396905	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49508103	rs9463500	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49515525	rs4715136	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49518914	rs6919674	C	G	44.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=2.303;VQSLOD=8.57;culprit=FS;GENE=C6orf141	GT:AD:DP:GQ:PL	1/1:0,2:2:6:72,6,0
-chr6	49522920	.	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=C6orf141	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49528183	rs6899583	A	G	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.73;culprit=FS;GENE=C6orf141	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	49537956	rs36081197	T	A	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.79;culprit=FS;GENE=CYP2AC1P	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	49559793	rs10948514	G	T	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	49596219	rs4711931	T	C	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.2;culprit=FS;GENE=RHAG	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	49646966	rs7763840	T	C	66.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=8.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	49650193	rs148454607	CCCT	C	84.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=62.13;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=6.11;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:37:122,0,37
-chr6	49660418	rs12624	A	C	1647.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.101;ClippingRankSum=-1.338;DB;DP=95;FS=5.883;MLEAC=1;MLEAF=0.5;MQ=59.76;MQ0=0;MQRankSum=-1.323;POSITIVE_TRAIN_SITE;QD=17.34;ReadPosRankSum=0.011;SOR=1.333;VQSLOD=1.55;culprit=FS;GENE=CRISP2	GT:AD:DP:GQ:PL	0/1:42,53:95:99:1676,0,1201
-chr6	49663465	rs2248263	G	A	603.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.236;ClippingRankSum=0.133;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.43;MQ0=0;MQRankSum=0.399;POSITIVE_TRAIN_SITE;QD=18.3;ReadPosRankSum=0.589;SOR=0.957;VQSLOD=5.69;culprit=FS;GENE=CRISP2	GT:AD:DP:GQ:PL	0/1:14,18:32:99:632,0,410
-chr6	49665120	rs10548881	GGT	G	34.71	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=2.303;VQSLOD=8.54;culprit=FS;GENE=CRISP2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
-chr6	49666381	rs515257	G	A	145.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.886;ClippingRankSum=-1.798;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=7.67;ReadPosRankSum=1.184;SOR=0.223;VQSLOD=5.06;culprit=QD;GENE=CRISP2	GT:AD:DP:GQ:PL	0/1:13,6:19:99:174,0,478
-chr6	49668405	rs57295760	T	G	1149.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.101;ClippingRankSum=0.57;DB;DP=174;FS=322.757;MLEAC=1;MLEAF=0.5;MQ=47.79;MQ0=0;MQRankSum=-5.344;QD=6.61;ReadPosRankSum=-6.45;SOR=9.149;VQSLOD=-248.5;culprit=FS;GENE=CRISP2	GT:AD:DP:GQ:PL	0/1:77,96:173:99:1178,0,1978
-chr6	49676536	rs699954	C	T	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.45;culprit=FS;GENE=CRISP2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	49693598	rs1068276	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49693612	rs35883674	CT	C	93.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.08;SOR=1.179;VQSLOD=8.8;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	49695232	rs510770	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CRISP3	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49701439	rs1864312	C	A	1555.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.745;ClippingRankSum=0.346;DB;DP=113;FS=1.849;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.795;POSITIVE_TRAIN_SITE;QD=13.77;ReadPosRankSum=1.613;SOR=0.978;VQSLOD=2.84;culprit=ReadPosRankSum;GENE=CRISP3	GT:AD:DP:GQ:PL	0/1:63,49:112:99:1584,0,2066
-chr6	49701523	rs495335	A	G	1861.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.084;ClippingRankSum=-0.565;DB;DP=149;FS=0.622;MLEAC=1;MLEAF=0.5;MQ=59.85;MQ0=0;MQRankSum=-0.4;POSITIVE_TRAIN_SITE;QD=12.5;ReadPosRankSum=3.925;SOR=0.775;VQSLOD=2.06;culprit=ReadPosRankSum;GENE=CRISP3	GT:AD:DP:GQ:PL	0/1:84,65:149:99:1890,0,2674
-chr6	49703027	rs3823210	G	T	73.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=14.75;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=6.26;culprit=FS;GENE=CRISP3	GT:AD:DP:GQ:PL	0/1:2,3:5:72:102,0,72
-chr6	49787315	rs5876131	G	GT	25.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.86;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:62,6,0
-chr6	49798102	.	C	CAGAG	53.7	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=4.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49803370	rs1652094	A	G	290.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.34;SOR=4.407;VQSLOD=6.61;culprit=FS;GENE=CRISP1	GT:AD:DP:GQ:PL	1/1:0,8:8:24:319,24,0
-chr6	49807422	rs7753886	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CRISP1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49815873	rs373553362	AT	A	85.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.243;ClippingRankSum=-0.384;DB;DP=85;FS=2.397;MLEAC=1;MLEAF=0.5;MQ=57.35;MQ0=0;MQRankSum=1.2;QD=1.01;ReadPosRankSum=0.512;SOR=1.508;VQSLOD=1.09;culprit=MQRankSum;GENE=CRISP1	GT:AD:DP:GQ:PL	0/1:52,14:66:99:123,0,1132
-chr6	49818670	rs780782	T	C	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.96;culprit=FS;GENE=CRISP1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	49835335	rs1084051	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CRISP1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49858594	rs2153575	C	T	361.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.037;ClippingRankSum=1.977;DB;DP=21;FS=4.722;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.037;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.336;SOR=0.127;VQSLOD=3.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:390,0,186
-chr6	49913981	rs7760672	C	T	1758.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.016;ClippingRankSum=0.747;DB;DP=119;FS=1.762;MLEAC=1;MLEAF=0.5;MQ=59.81;MQ0=0;MQRankSum=0.359;POSITIVE_TRAIN_SITE;QD=14.78;ReadPosRankSum=-0.178;SOR=0.963;VQSLOD=3.22;culprit=DP;GENE=DEFB133	GT:AD:DP:GQ:PL	0/1:58,61:119:99:1787,0,1869
-chr6	49917264	rs9369926	A	C	219.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.22;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.732;POSITIVE_TRAIN_SITE;QD=12.93;ReadPosRankSum=1.317;SOR=0.425;VQSLOD=5.32;culprit=FS;GENE=DEFB133	GT:AD:DP:GQ:PL	0/1:10,7:17:99:248,0,336
-chr6	49956510	.	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50045305	rs1324514	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50064359	rs9395549	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50087752	rs6458721	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50155014	.	T	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:29:40,0,29
-chr6	50155159	rs700005	A	C	44.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=0.693;VQSLOD=8.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:72,6,0
-chr6	50158759	rs142079970	G	GT	21.73	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0
-chr6	50164244	rs9369936	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50169217	rs148924218	C	CT	19.75	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=9.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:56,6,0
-chr6	50197539	rs6910805	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50222518	rs1340844	T	C	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	50225593	rs9349526	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50230041	rs1596084	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50230068	rs7756066	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50231408	rs6903689	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50261294	rs2792835	T	C	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	50265655	rs5876165	GA	G	21.73	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=10.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0
-chr6	50294995	rs10637978	A	ATAATT	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	50298895	rs7775569	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50325057	rs2131281	G	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.1;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	50362460	rs7745382	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50364398	rs6930590	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50366720	rs7738992	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50650700	rs537362	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50805942	rs2817404	T	G	938.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=23;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.99;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.85;SOR=6.358;VQSLOD=6.9;culprit=FS;GENE=TFAP2B	GT:AD:DP:GQ:PL	1/1:0,23:23:69:967,69,0
-chr6	50810497	rs1569778	T	C	85.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.43;SOR=2.833;VQSLOD=7.71;culprit=FS;GENE=TFAP2B	GT:AD:DP:GQ:PL	1/1:0,3:3:9:113,9,0
-chr6	50811241	rs2982621	T	A	306.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=4.615;VQSLOD=5.67;culprit=FS;GENE=TFAP2B	GT:AD:DP:GQ:PL	1/1:0,9:9:27:335,27,0
-chr6	50812003	rs35732696	TA	T	11.99	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=4.0;SOR=2.303;GENE=TFAP2B	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	50824804	rs2817423	T	A	1009.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=6.666;VQSLOD=5.96;culprit=FS;GENE=RPS17P5	GT:AD:DP:GQ:PL	1/1:0,27:27:81:1038,81,0
-chr6	50866066	rs11754505	C	T	130.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.51;SOR=1.609;VQSLOD=7.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:158,12,0
-chr6	50880250	rs61678343	C	CT	116.87	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.73;MQ0=0;QD=16.7;SOR=3.611;VQSLOD=5.12;culprit=FS;GENE=FTH1P5	GT:AD:DP:GQ:PL	1/1:0,5:5:15:154,15,0
-chr6	50886019	rs75756982	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.5;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50966615	rs557411	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51003728	rs140549964	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51003757	.	T	A	62.74	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51003762	rs145721769	T	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51162298	rs1409888	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51171408	rs1327265	G	A	95.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=9.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	51173538	rs2256042	G	A	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.75;SOR=1.179;VQSLOD=8.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	51173541	rs2256041	A	G	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.8;SOR=1.179;VQSLOD=8.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	51199224	rs2796913	T	C	136.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.38;SOR=1.981;VQSLOD=6.3;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:165,15,0
-chr6	51274751	.	CTT	C	59.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.55;ClippingRankSum=1.3;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.1;MQ0=0;MQRankSum=-0.937;QD=5.43;ReadPosRankSum=0.55;SOR=0.223;VQSLOD=4.67;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:51:97,0,51
-chr6	51317602	rs9367432	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51329696	rs3928895	G	C	93.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	51339492	rs4090367	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51434479	rs4997737	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.32;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51434483	rs181171044	A	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51446475	rs2495854	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51492046	rs9474033	T	G	2499.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=62;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.45;SOR=8.287;VQSLOD=5.75;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2528,187,0
-chr6	51492164	rs9370040	T	A	258.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.68;SOR=4.174;VQSLOD=6.27;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,7:7:21:287,21,0
-chr6	51503597	.	C	CAAA	667.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.313;ClippingRankSum=-1.388;DP=300;FS=6.792;MLEAC=1;MLEAF=0.5;MQ=49.95;MQ0=0;MQRankSum=-2.762;NEGATIVE_TRAIN_SITE;QD=2.23;ReadPosRankSum=-2.418;SOR=0.016;VQSLOD=-2.167;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:77,45:122:99:705,0,1544
-chr6	51512707	rs2580009	T	C	944.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=26;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.11;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.22;SOR=6.593;VQSLOD=5.86;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,26:26:78:973,78,0
-chr6	51521787	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51523739	rs115072237	T	C	6637.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=176;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.68;SOR=2.371;VQSLOD=5.0;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,175:175:99:6666,526,0
-chr6	51551346	rs557398	T	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.05;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	51590078	rs1326610	T	C	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.76;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	51604677	.	C	T	956.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.698;ClippingRankSum=-0.058;DP=66;FS=6.929;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.341;QD=14.5;ReadPosRankSum=1.938;SOR=0.066;VQSLOD=0.46;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:36,30:66:99:985,0,1262
-chr6	51606225	rs142928645	C	T	114.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-1.38;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.38;POSITIVE_TRAIN_SITE;QD=19.13;ReadPosRankSum=0.72;SOR=1.329;VQSLOD=4.76;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:2,4:6:59:143,0,59
-chr6	51611733	rs200125913	A	C	194.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.113;ClippingRankSum=1.133;DB;DP=24;FS=9.938;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=-0.153;NEGATIVE_TRAIN_SITE;QD=8.12;ReadPosRankSum=0.643;SOR=3.99;VQSLOD=-1.655;culprit=QD;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:8,16:24:99:223,0,155
-chr6	51617800	rs1326607	A	G	332.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=10;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.28;SOR=4.804;VQSLOD=6.82;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,10:10:30:361,30,0
-chr6	51634407	.	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51640751	rs3920621	C	G	1527.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.616;ClippingRankSum=-0.475;DB;DP=114;FS=5.314;MLEAC=1;MLEAF=0.5;MQ=59.67;MQ0=0;MQRankSum=-1.12;POSITIVE_TRAIN_SITE;QD=13.4;ReadPosRankSum=-0.393;SOR=0.217;VQSLOD=1.32;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:63,49:112:99:1556,0,2311
-chr6	51649062	rs11435548	G	GT	58.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.42;SOR=1.179;VQSLOD=7.95;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:95,9,0
-chr6	51649079	rs4715232	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=7.4;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	51652585	rs1326561	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=7.54;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51652595	rs1326562	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.18;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51655796	rs6904634	T	C	99.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.93;SOR=2.303;VQSLOD=6.99;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:9:127,9,0
-chr6	51655803	rs6924716	C	T	99.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=2.833;VQSLOD=7.69;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:127,9,0
-chr6	51656236	rs7765455	G	T	1483.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=40;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.49;SOR=3.611;VQSLOD=5.62;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1512,120,0
-chr6	51656388	rs4715233	A	G	93.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.93;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	51664791	rs1980834	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51664816	rs2148459	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51671321	rs1326584	T	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.93;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	51671350	rs4470847	C	G	66.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=9.01;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	51673939	rs1326588	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51706167	rs10648630	C	CCCTTT	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.9;SOR=0.693;VQSLOD=8.28;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51712492	rs9370067	A	T	1705.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=42;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.14;SOR=7.523;VQSLOD=6.66;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1734,126,0
-chr6	51718857	rs1831015	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51720838	rs9349603	T	C	7371.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=189;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.858;VQSLOD=4.99;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,185:185:99:7400,557,0
-chr6	51720872	rs7452724	A	G	6199.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=161;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.66;SOR=3.188;VQSLOD=6.56;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,161:161:99:6228,484,0
-chr6	51723015	rs9370074	G	A	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=7.56;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	51732598	rs9382043	G	A	2712.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.5;SOR=3.026;VQSLOD=5.85;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,74:74:99:2741,222,0
-chr6	51732628	rs9382044	G	A	3330.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=89;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.74;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.8;SOR=2.276;VQSLOD=6.28;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3359,267,0
-chr6	51735261	rs982874	G	T	2752.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=73;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.4;SOR=4.558;VQSLOD=6.0;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2781,220,0
-chr6	51735613	rs2064871	T	C	314.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.95;SOR=4.407;VQSLOD=6.77;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,8:8:24:343,24,0
-chr6	51747589	rs6458801	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51750563	rs4711985	A	T	498.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.32;SOR=5.283;VQSLOD=6.36;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,13:13:39:527,39,0
-chr6	51757014	rs1321516	C	T	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.44;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	51768630	rs141063789	CATATAT	C	229.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=22;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.71;MQ0=0;POSITIVE_TRAIN_SITE;QD=10.44;SOR=2.303;VQSLOD=6.39;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,6:6:20:267,20,0
-chr6	51791091	rs4711990	G	T	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.23;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	51793425	rs5876244	C	CA	44.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.4;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	51796751	rs3857602	G	A	89.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=1.179;VQSLOD=5.58;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:117,9,0
-chr6	51798753	rs1266888	G	A	308.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.9;SOR=4.407;VQSLOD=6.3;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,8:8:24:337,24,0
-chr6	51798760	rs1884953	T	A	94.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=9.48;ReadPosRankSum=-0.365;SOR=0.412;VQSLOD=6.15;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:6,4:10:99:123,0,204
-chr6	51799166	rs1266889	T	C	1497.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=38;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.26;SOR=4.977;VQSLOD=5.51;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,37:37:99:1526,111,0
-chr6	51800445	rs1266890	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51814216	rs4715264	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.34;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51814217	rs1266913	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.56;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51844368	rs2435324	A	G	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.63;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	51856374	rs9463746	A	G	45.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.12;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	51875250	rs2435322	A	C	4902.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=132;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.68;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=1.17;VQSLOD=5.57;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,130:130:99:4931,391,0
-chr6	51882075	rs9349614	C	G	29.77	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.067;ClippingRankSum=0.572;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.589;QD=3.31;ReadPosRankSum=0.572;SOR=0.169;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:6,2:8:58:58,0,201
-chr6	51889483	rs45517932	G	A	1402.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.623;ClippingRankSum=-0.441;DB;DP=91;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.758;QD=15.42;ReadPosRankSum=0.099;SOR=0.684;VQSLOD=3.39;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:47,44:91:99:1431,0,1559
-chr6	51890823	rs9296669	G	A	908.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.796;ClippingRankSum=-1.279;DB;DP=60;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=0.614;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=0.052;SOR=0.575;VQSLOD=5.85;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:30,30:60:99:937,0,937
-chr6	51891011	rs2499480	T	C	1469.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.48;ClippingRankSum=1.669;DB;DP=99;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.53;MQ0=0;MQRankSum=-0.671;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=0.425;SOR=0.787;VQSLOD=5.12;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:54,45:99:99:1498,0,1703
-chr6	51913240	rs10948667	G	A	2227.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.872;ClippingRankSum=0.978;DB;DP=133;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.127;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=0.314;SOR=0.691;VQSLOD=4.01;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:61,72:133:99:2256,0,2006
-chr6	51914898	rs9395759	T	C	962.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.45;SOR=5.211;VQSLOD=6.92;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,27:27:81:991,81,0
-chr6	51914956	rs9370096	G	A	738.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.924;ClippingRankSum=-1.239;DB;DP=57;FS=1.721;MLEAC=1;MLEAF=0.5;MQ=53.16;MQ0=0;MQRankSum=-2.997;POSITIVE_TRAIN_SITE;QD=12.96;ReadPosRankSum=0.567;SOR=1.274;VQSLOD=0.74;culprit=MQRankSum;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:30,27:57:99:767,0,838
-chr6	51917550	rs1896983	G	A	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.73;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	51923569	rs56342114	CTCTA	C	188.84	PASS	AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.74;SOR=3.611;VQSLOD=5.56;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,5:5:16:226,16,0
-chr6	51924774	rs1896976	A	G	11214.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=307;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.73;SOR=0.923;VQSLOD=3.9;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,306:306:99:11243,918,0
-chr6	51927683	rs13198604	T	C	130.79	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=21.8;ReadPosRankSum=0.736;SOR=0.941;VQSLOD=5.66;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:1,5:6:22:159,0,22
-chr6	51930886	rs5876252	T	TA	1123.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.558;ClippingRankSum=0.596;DB;DP=98;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.11;MQ0=0;MQRankSum=0.066;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.047;SOR=1.571;VQSLOD=5.61;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:14,49:63:99:1161,0,109
-chr6	51935061	rs4711996	T	G	632.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.75;SOR=5.67;VQSLOD=6.32;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,16:16:48:661,48,0
-chr6	51935747	rs17576809	C	T	1555.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.681;ClippingRankSum=0.579;DB;DP=78;FS=1.884;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=2.282;SOR=1.437;VQSLOD=1.66;culprit=ReadPosRankSum;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:34,44:78:99:1584,0,1003
-chr6	51936846	rs3936986	T	C	1197.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.52;ClippingRankSum=2.065;DB;DP=65;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=-0.165;POSITIVE_TRAIN_SITE;QD=18.43;ReadPosRankSum=-0.31;SOR=0.499;VQSLOD=5.41;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:29,36:65:99:1226,0,894
-chr6	51938242	rs9474140	A	G	2915.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.879;ClippingRankSum=-1.66;DB;DP=204;FS=1.266;MLEAC=1;MLEAF=0.5;MQ=59.55;MQ0=0;MQRankSum=0.616;POSITIVE_TRAIN_SITE;QD=14.29;ReadPosRankSum=0.116;SOR=0.846;VQSLOD=2.35;culprit=DP;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:112,92:204:99:2944,0,3367
-chr6	51944847	rs1892274	T	C	1304.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.941;ClippingRankSum=0.488;DB;DP=91;FS=6.922;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-0.933;POSITIVE_TRAIN_SITE;QD=14.34;ReadPosRankSum=0.242;SOR=2.14;VQSLOD=2.08;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:45,46:91:99:1333,0,1431
-chr6	51946893	rs6458806	T	C	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.64;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	51947237	rs9474143	G	A	5131.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.494;ClippingRankSum=0.221;DB;DP=273;FS=2.813;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.398;POSITIVE_TRAIN_SITE;QD=18.8;ReadPosRankSum=1.871;SOR=0.538;VQSLOD=1.29;culprit=DP;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:114,158:272:99:5160,0,3305
-chr6	51949862	rs9370097	A	G	953.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.068;ClippingRankSum=-1.115;DB;DP=65;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.363;POSITIVE_TRAIN_SITE;QD=14.67;ReadPosRankSum=-0.917;SOR=0.505;VQSLOD=5.49;culprit=FS;GENE=PKHD1	GT:AD:DP:GQ:PL	0/1:36,29:65:99:982,0,1231
-chr6	51953191	rs6905678	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51963443	rs6914462	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51971195	rs3997006	T	C	91.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=7.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	51997155	rs1892278	A	C	327.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.056;VQSLOD=5.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:27:356,27,0
-chr6	52054249	rs7747909	G	A	105.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.421;ClippingRankSum=0.922;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.017;POSITIVE_TRAIN_SITE;QD=13.22;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=4.45;culprit=FS;GENE=IL17A	GT:AD:DP:GQ:PL	0/1:4,4:8:99:134,0,134
-chr6	52061133	rs11962054	A	G	16.63	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.63;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	52064989	rs11755816	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52065009	rs11751159	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52073500	rs4464776	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52075816	rs2397079	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=9.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	52085748	rs591274	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52111808	rs761167	C	T	630.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.571;ClippingRankSum=-0.018;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.3;MQ0=0;MQRankSum=0.792;POSITIVE_TRAIN_SITE;QD=19.11;ReadPosRankSum=0.534;SOR=0.743;VQSLOD=5.64;culprit=FS;GENE=SLC25A20P1	GT:AD:DP:GQ:PL	0/1:13,20:33:99:659,0,402
-chr6	52117224	rs604952	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52129484	rs2230240	C	T	3990.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.023;ClippingRankSum=-0.723;DB;DP=236;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.012;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.682;SOR=0.712;VQSLOD=1.85;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:105,131:236:99:4019,0,2992
-chr6	52129667	rs2307326	G	A	917.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.356;ClippingRankSum=-0.312;DB;DP=53;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.791;POSITIVE_TRAIN_SITE;QD=17.32;ReadPosRankSum=-2.147;SOR=0.808;VQSLOD=3.93;culprit=ReadPosRankSum;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:25,28:53:99:946,0,873
-chr6	52130745	rs6925229	T	C	162.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.139;ClippingRankSum=1.898;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=10.17;ReadPosRankSum=0.597;SOR=0.34;VQSLOD=6.23;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:10,6:16:99:191,0,354
-chr6	52131254	rs10807441	C	T	1383.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.953;ClippingRankSum=0.77;DB;DP=83;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.223;POSITIVE_TRAIN_SITE;QD=16.67;ReadPosRankSum=0.269;SOR=1.534;VQSLOD=5.05;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:43,40:83:99:1412,0,1442
-chr6	52137313	rs12207056	C	T	464.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.684;ClippingRankSum=-0.306;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.56;MQ0=0;MQRankSum=-0.162;POSITIVE_TRAIN_SITE;QD=14.08;ReadPosRankSum=1.207;SOR=1.609;VQSLOD=5.72;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:17,16:33:99:493,0,518
-chr6	52138441	rs6918669	G	A	286.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.355;ClippingRankSum=-0.442;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.971;SOR=1.781;VQSLOD=6.47;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:9,9:18:99:315,0,267
-chr6	52141670	rs3765446	A	T	142.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.635;ClippingRankSum=1.0;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.134;POSITIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=0.135;SOR=1.371;VQSLOD=6.12;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:7,5:12:99:171,0,247
-chr6	52142092	rs2307325	C	T	222.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.092;ClippingRankSum=0.092;DB;DP=24;FS=1.999;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.276;POSITIVE_TRAIN_SITE;QD=9.28;ReadPosRankSum=0.704;SOR=1.214;VQSLOD=2.73;culprit=QD;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:16,8:24:99:251,0,540
-chr6	52142582	rs13191372	G	A	424.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.394;ClippingRankSum=0.496;DB;DP=31;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.5;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=13.7;ReadPosRankSum=1.409;SOR=0.527;VQSLOD=5.12;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:17,14:31:99:453,0,593
-chr6	52143987	rs2076510	C	T	232.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.78;ClippingRankSum=-0.625;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.241;POSITIVE_TRAIN_SITE;QD=13.69;ReadPosRankSum=1.973;SOR=0.593;VQSLOD=5.87;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:9,8:17:99:261,0,314
-chr6	52144081	rs2073036	T	C	952.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.283;ClippingRankSum=-0.724;DB;DP=63;FS=1.092;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.193;POSITIVE_TRAIN_SITE;QD=15.12;ReadPosRankSum=0.145;SOR=0.485;VQSLOD=2.82;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:29,34:63:99:981,0,911
-chr6	52147271	rs7756989	T	C	20.8	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=1.38;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.72;QD=3.47;ReadPosRankSum=0.72;SOR=0.693;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:4,2:6:49:49,0,109
-chr6	52147363	rs12202495	A	G	191.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.279;ClippingRankSum=0.579;DB;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.193;POSITIVE_TRAIN_SITE;QD=9.59;ReadPosRankSum=1.042;SOR=0.392;VQSLOD=5.45;culprit=FS;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:12,8:20:99:220,0,424
-chr6	52147692	rs2307322	T	A	893.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.042;ClippingRankSum=0.16;DB;DP=47;FS=9.107;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.46;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=3.166;SOR=2.472;VQSLOD=0.472;culprit=ReadPosRankSum;GENE=MCM3	GT:AD:DP:GQ:PL	0/1:22,25:47:99:922,0,588
-chr6	52148465	rs9474192	T	G	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.21;culprit=QD;GENE=MCM3	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	52217185	rs9395785	C	G	142.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.922;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.495;POSITIVE_TRAIN_SITE;QD=20.4;ReadPosRankSum=0.922;SOR=1.609;VQSLOD=5.94;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,5:7:66:171,0,66
-chr6	52240487	rs6458837	G	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.88;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	52245945	rs71794438	CA	C	38.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=2.303;VQSLOD=7.53;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	52257835	rs669893	A	G	17.61	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.61;SOR=1.609;GENE=PAQR8	GT:AD:DP:GQ:PL	1/1:0,1:1:3:44,3,0
-chr6	52257856	rs526553	G	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.49;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	52267967	rs76408349	A	C	39.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=1.231;POSITIVE_TRAIN_SITE;QD=7.95;ReadPosRankSum=-0.358;SOR=0.446;VQSLOD=5.7;culprit=QD;GENE=PAQR8	GT:AD:DP:GQ:PL	0/1:3,2:5:68:68,0,92
-chr6	52268008	rs3748066	T	G	117.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=16.82;ReadPosRankSum=-0.922;SOR=0.527;VQSLOD=6.33;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	0/1:2,5:7:62:146,0,62
-chr6	52268086	rs146353145	C	T	319.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.458;ClippingRankSum=-0.387;DB;DP=21;FS=3.222;MLEAC=1;MLEAF=0.5;MQ=57.77;MQ0=0;MQRankSum=-0.81;QD=15.23;ReadPosRankSum=0.599;SOR=1.911;VQSLOD=1.55;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	0/1:10,11:21:99:348,0,301
-chr6	52268890	rs17591381	G	A	546.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.06;ClippingRankSum=0.774;DB;DP=49;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.58;MQ0=0;MQRankSum=1.035;POSITIVE_TRAIN_SITE;QD=11.16;ReadPosRankSum=0.794;SOR=0.712;VQSLOD=5.57;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	0/1:27,22:49:99:575,0,819
-chr6	52269199	rs3799272	T	C	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.07;culprit=FS;GENE=PAQR8	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	52296461	rs1840169	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EFHC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52319251	rs614570	C	T	274.18	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.751;POSITIVE_TRAIN_SITE;QD=30.46;ReadPosRankSum=0.751;SOR=3.056;VQSLOD=5.38;culprit=FS;GENE=EFHC1	GT:AD:DP:GQ:PL	0/1:1,8:9:10:302,0,10
-chr6	52355206	rs2273120	T	C	1095.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=30;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.353;VQSLOD=6.99;culprit=FS;GENE=EFHC1	GT:AD:DP:GQ:PL	1/1:0,29:29:87:1124,87,0
-chr6	52357260	rs7757370	C	A	601.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.84;SOR=5.67;VQSLOD=6.12;culprit=FS;GENE=EFHC1	GT:AD:DP:GQ:PL	1/1:0,16:16:48:630,48,0
-chr6	52367845	rs3032	C	T	381.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.028;ClippingRankSum=0.927;DB;DP=24;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.03;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=15.91;ReadPosRankSum=-0.348;SOR=0.859;VQSLOD=5.92;culprit=FS;GENE=EFHC1,TRAM2	GT:AD:DP:GQ:PL	0/1:11,13:24:99:410,0,338
-chr6	52370939	rs9688915	G	A	1148.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.52;ClippingRankSum=1.052;DB;DP=64;FS=1.426;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.175;POSITIVE_TRAIN_SITE;QD=17.95;ReadPosRankSum=0.836;SOR=1.212;VQSLOD=2.7;culprit=ReadPosRankSum;GENE=EFHC1,TRAM2	GT:AD:DP:GQ:PL	0/1:29,35:64:99:1177,0,853
-chr6	52380641	rs941968	C	T	424.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.39;ClippingRankSum=-1.102;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.603;SOR=0.576;VQSLOD=5.79;culprit=FS;GENE=EFHC1,TRAM2	GT:AD:DP:GQ:PL	0/1:16,14:30:99:453,0,559
-chr6	52381728	rs6917085	A	T	86.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=-0.727;SOR=1.609;VQSLOD=6.1;culprit=FS;GENE=EFHC1,TRAM2	GT:AD:DP:GQ:PL	0/1:1,3:4:32:115,0,32
-chr6	52425189	rs7744675	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=TRAM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52433894	rs55959984	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=TRAM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52451301	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52453985	rs9370135	T	A	42.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:30:71,0,30
-chr6	52469904	rs9463802	A	G	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.2;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	52475696	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52483058	rs11755043	C	A	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.1;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	52538160	rs55704840	A	AG	38.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.83;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	52538171	rs7746344	A	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.58;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	52538198	rs9349638	T	A	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=0.693;VQSLOD=7.1;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	52538242	rs9349639	T	G	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=7.79;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	52538390	rs9349640	T	C	45.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=8.54;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	52541811	rs13211066	G	A	2092.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=52;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=7.941;VQSLOD=6.16;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2121,157,0
-chr6	52546789	rs2281484	C	T	1421.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=38;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.25;SOR=7.328;VQSLOD=7.46;culprit=FS;GENE=TMEM14A	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1450,114,0
-chr6	52553436	rs9382133	C	T	766.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.752;ClippingRankSum=0.06;DB;DP=45;FS=4.452;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=0.37;POSITIVE_TRAIN_SITE;QD=17.04;ReadPosRankSum=0.418;SOR=1.118;VQSLOD=2.96;culprit=FS;GENE=GSTA8P	GT:AD:DP:GQ:PL	0/1:18,26:44:99:795,0,532
-chr6	52565427	rs4637643	T	G	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.3;culprit=FS;GENE=GSTA8P	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	52568775	rs6909894	G	C	181.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=1.981;VQSLOD=6.47;culprit=FS;GENE=GSTA8P	GT:AD:DP:GQ:PL	1/1:0,5:5:15:210,15,0
-chr6	52568848	rs36098646	G	GA	25.95	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=62.65;MQ0=0;MQRankSum=0.727;QD=6.49;ReadPosRankSum=0.727;SOR=0.916;GENE=GSTA8P	GT:AD:DP:GQ:PL	0/1:1,3:4:13:63,0,13
-chr6	52615371	rs199546282	T	G	302.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.16;ClippingRankSum=-0.23;DB;DP=163;FS=296.91;MLEAC=1;MLEAF=0.5;MQ=54.98;MQ0=0;MQRankSum=-0.947;QD=1.86;ReadPosRankSum=-4.824;SOR=8.189;VQSLOD=-199.5;culprit=FS;GENE=GSTA2	GT:AD:DP:GQ:PL	0/1:103,59:162:99:331,0,2945
-chr6	52616633	rs72934249	C	T	667.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.954;ClippingRankSum=0.781;DB;DP=47;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=0.909;POSITIVE_TRAIN_SITE;QD=14.21;ReadPosRankSum=-0.631;SOR=0.509;VQSLOD=5.18;culprit=FS;GENE=GSTA2	GT:AD:DP:GQ:PL	0/1:26,21:47:99:696,0,789
-chr6	52617731	rs2180314	C	G	6239.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.736;ClippingRankSum=-0.69;DB;DP=405;FS=1.2;MLEAC=1;MLEAF=0.5;MQ=59.74;MQ0=0;MQRankSum=-0.793;POSITIVE_TRAIN_SITE;QD=15.41;ReadPosRankSum=1.185;SOR=0.583;VQSLOD=1.22;culprit=DP;GENE=GSTA2	GT:AD:DP:GQ:PL	0/1:207,197:404:99:6268,0,6969
-chr6	52622475	rs2608624	G	T	277.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.387;ClippingRankSum=-0.529;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.529;POSITIVE_TRAIN_SITE;QD=17.36;ReadPosRankSum=-1.482;SOR=0.941;VQSLOD=4.88;culprit=FS;GENE=GSTA2	GT:AD:DP:GQ:PL	0/1:7,9:16:99:306,0,255
-chr6	52622814	rs2254050	C	T	889.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.466;ClippingRankSum=2.068;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.456;POSITIVE_TRAIN_SITE;QD=17.8;ReadPosRankSum=0.651;SOR=0.773;VQSLOD=5.34;culprit=FS;GENE=GSTA2	GT:AD:DP:GQ:PL	0/1:24,26:50:99:918,0,713
-chr6	52630153	rs6458868	C	T	560.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.03;ClippingRankSum=-0.43;DB;DP=42;FS=1.283;MLEAC=1;MLEAF=0.5;MQ=56.17;MQ0=0;MQRankSum=0.483;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=2.308;SOR=1.064;VQSLOD=2.33;culprit=ReadPosRankSum;GENE=GSTA12P	GT:AD:DP:GQ:PL	0/1:21,20:41:99:589,0,560
-chr6	52630269	rs6458869	C	A	534.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.861;ClippingRankSum=-1.139;DB;DP=26;FS=1.757;MLEAC=1;MLEAF=0.5;MQ=49.59;MQ0=0;MQRankSum=-2.083;POSITIVE_TRAIN_SITE;QD=20.57;ReadPosRankSum=-0.583;SOR=0.346;VQSLOD=1.61;culprit=MQRankSum;GENE=GSTA12P	GT:AD:DP:GQ:PL	0/1:8,18:26:99:563,0,197
-chr6	52631188	rs2749029	A	G	696.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.911;ClippingRankSum=0.581;DB;DP=58;FS=2.243;MLEAC=1;MLEAF=0.5;MQ=59.68;MQ0=0;MQRankSum=-0.722;POSITIVE_TRAIN_SITE;QD=12.01;ReadPosRankSum=0.581;SOR=0.416;VQSLOD=2.99;culprit=QD;GENE=GSTA12P	GT:AD:DP:GQ:PL	0/1:33,25:58:99:725,0,1078
-chr6	52655827	rs6904269	G	A	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=9.25;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	52657321	rs4147615	T	C	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.21;culprit=DP;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	52658962	rs1051775	T	C	16388.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.0;AN=2;BaseQRankSum=1.724;ClippingRankSum=-0.564;DB;DP=430;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.91;MQ0=0;MQRankSum=0.177;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=26.2;ReadPosRankSum=0.878;SOR=0.736;VQSLOD=-0.8417;culprit=DP;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:1,429:430:99:16417,1283,0
-chr6	52660828	rs2894803	C	A	2866.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.91;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=8.608;VQSLOD=6.77;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2895,220,0
-chr6	52661267	.	ATATATATATATATATATATATGTGTG	A	235.79	PASS	AC=2;AF=1.0;AN=2;DP=21;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=43.56;MQ0=0;QD=11.23;SOR=3.912;VQSLOD=4.84;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,6:6:19:273,19,0
-chr6	52662263	rs2397106	C	T	1326.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=39;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=41.5;MQ0=0;QD=34.02;SOR=5.892;VQSLOD=5.23;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1355,114,0
-chr6	52662568	rs139503836	G	A	365.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.392;ClippingRankSum=-0.198;DB;DP=36;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.74;MQ0=0;MQRankSum=-1.778;QD=10.16;ReadPosRankSum=1.12;SOR=0.293;VQSLOD=2.34;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	0/1:23,13:36:99:394,0,797
-chr6	52663705	rs9349644	C	T	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.95;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	52663813	rs10948722	A	G	801.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=20;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=6.091;VQSLOD=6.69;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	1/1:0,20:20:60:830,60,0
-chr6	52664133	.	T	C	1090.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.013;ClippingRankSum=-0.873;DP=57;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.328;QD=19.14;ReadPosRankSum=0.377;SOR=0.285;VQSLOD=3.89;culprit=FS;GENE=GSTA1	GT:AD:DP:GQ:PL	0/1:26,31:57:99:1119,0,874
-chr6	52670630	rs10807454	A	C	691.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.81;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.23;SOR=3.258;VQSLOD=6.57;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:0,16:16:48:720,48,0
-chr6	52670633	rs62412861	A	G	725.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.81;MQ0=0;QD=24.12;SOR=3.258;VQSLOD=4.49;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:0,16:16:51:754,51,0
-chr6	52670639	rs62412870	C	T	680.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.44;MQ0=0;QD=29.35;SOR=3.258;VQSLOD=4.94;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:0,16:16:48:709,48,0
-chr6	52677230	rs5876288	G	GA	2040.73	PASS	AC=2;AF=1.0;AN=2;BaseQRankSum=-0.42;ClippingRankSum=0.166;DB;DP=129;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.66;MQ0=0;MQRankSum=0.381;POSITIVE_TRAIN_SITE;QD=15.82;ReadPosRankSum=-0.674;SOR=1.636;VQSLOD=4.43;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:6,81:87:99:2070,156,0
-chr6	52678337	rs6458873	G	T	1706.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=44;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.33;VQSLOD=6.87;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1735,132,0
-chr6	52678463	rs6458874	C	T	360.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=10;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.66;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.2;SOR=4.804;VQSLOD=6.59;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:0,10:10:30:389,30,0
-chr6	52678500	rs6458875	C	G	82.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.43;SOR=2.833;VQSLOD=8.62;culprit=FS;GENE=GSTA6P	GT:AD:DP:GQ:PL	1/1:0,3:3:9:110,9,0
-chr6	52688905	rs2983232	G	T	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=13.72;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	52694086	rs4311507	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52695461	rs10948726	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.5;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52697601	rs55815585	T	G	3617.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=94;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.68;SOR=2.354;VQSLOD=5.15;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,92:92:99:3646,277,0
-chr6	52697825	rs4715345	A	C	5351.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=123;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.29;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.62;SOR=2.226;VQSLOD=5.04;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,122:122:99:5380,367,0
-chr6	52697834	rs4715346	C	A	5365.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=120;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.25;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.36;SOR=2.507;VQSLOD=5.69;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,120:120:99:5394,370,0
-chr6	52697890	rs4715347	C	T	2514.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=5.042;VQSLOD=6.95;culprit=QD;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,65:65:99:2543,195,0
-chr6	52698035	rs4715348	A	G	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.47;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	52698653	rs6458880	C	T	131.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=3.258;VQSLOD=7.46;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,4:4:12:159,12,0
-chr6	52698788	rs4712021	T	C	3962.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=88;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.39;SOR=8.977;VQSLOD=6.17;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,88:88:99:3991,271,0
-chr6	52698798	rs4715349	G	T	4293.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=99;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.06;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.88;SOR=9.21;VQSLOD=6.95;culprit=DP;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,99:99:99:4322,298,0
-chr6	52700920	rs2397117	T	C	5074.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=131;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=9.735;VQSLOD=6.59;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,129:129:99:5103,388,0
-chr6	52701143	rs2397118	C	T	12265.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=338;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.8;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.4;SOR=1.526;VQSLOD=2.73;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,337:337:99:12294,1013,0
-chr6	52701458	rs2397119	T	C	81.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=2.833;VQSLOD=7.99;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:109,9,0
-chr6	52701582	rs62412887	T	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.25;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	52701589	rs2397121	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	52702324	rs4715350	T	C	4926.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=136;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.3;SOR=3.048;VQSLOD=4.71;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,135:135:99:4955,406,0
-chr6	52702529	rs4715351	T	C	1973.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=48;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.8;SOR=7.743;VQSLOD=6.84;culprit=FS;GENE=GSTA5	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2002,141,0
-chr6	52712461	rs9296693	G	A	232.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.26;SOR=4.174;VQSLOD=3.81;culprit=FS;GENE=GSTA11P	GT:AD:DP:GQ:PL	1/1:0,7:7:21:261,21,0
-chr6	52712645	rs9296694	C	G	4081.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=107;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.14;SOR=2.812;VQSLOD=6.01;culprit=FS;GENE=GSTA11P	GT:AD:DP:GQ:PL	1/1:0,107:107:99:4110,322,0
-chr6	52713902	rs62412891	C	T	1799.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=47;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.94;SOR=3.958;VQSLOD=6.18;culprit=FS;GENE=GSTA11P	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1828,141,0
-chr6	52724654	rs9349647	C	T	94.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=2.833;VQSLOD=8.25;culprit=FS;GENE=GSTA11P	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	52735179	rs72938158	T	A	2626.77	PASS	AC=2;AF=1.0;AN=2;BaseQRankSum=1.785;ClippingRankSum=1.186;DB;DP=68;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;MQRankSum=-1.577;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.32;ReadPosRankSum=3.323;SOR=5.136;VQSLOD=0.542;culprit=ReadPosRankSum;GENE=GSTA11P	GT:AD:DP:GQ:PL	1/1:4,64:68:99:2655,186,0
-chr6	52743455	rs4715360	T	C	2478.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=62;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=8.287;VQSLOD=5.41;culprit=FS;GENE=GSTA10P	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2507,187,0
-chr6	52744741	rs13198332	G	A	498.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=14;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.93;SOR=0.693;VQSLOD=6.43;culprit=FS;GENE=GSTA10P	GT:AD:DP:GQ:PL	1/1:0,14:14:42:527,42,0
-chr6	52746642	rs72940404	G	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:30:40,0,30
-chr6	52761898	rs2295605	T	C	585.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=17;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.63;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.46;SOR=5.784;VQSLOD=7.27;culprit=FS;GENE=GSTA3	GT:AD:DP:GQ:PL	1/1:0,17:17:51:614,51,0
-chr6	52766192	rs6935603	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GSTA3	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52767869	rs542113	T	A	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.36;culprit=FS;GENE=GSTA3	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	52768392	.	CA	C	63.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.806;ClippingRankSum=-0.832;DP=73;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.1;MQ0=0;MQRankSum=1.36;QD=0.87;ReadPosRankSum=-1.466;SOR=0.111;VQSLOD=2.98;culprit=FS;GENE=GSTA3	GT:AD:DP:GQ:PL	0/1:42,11:53:99:101,0,838
-chr6	52785560	rs689167	G	A	446.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.37;SOR=0.836;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,13:13:39:475,39,0
-chr6	52785580	rs689197	G	A	546.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.17;SOR=0.693;VQSLOD=6.6;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:575,48,0
-chr6	52785649	rs581594	G	A	388.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=11;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.47;SOR=4.804;VQSLOD=6.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,10:10:30:417,30,0
-chr6	52795274	rs547362	G	T	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	52802244	rs371403	A	G	109.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.26;SOR=1.609;VQSLOD=7.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:137,12,0
-chr6	52820382	rs10948733	G	A	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.62;culprit=FS;GENE=GSTA9P	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	52835606	rs571672	T	C	114.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.51;SOR=3.258;VQSLOD=6.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:142,12,0
-chr6	52839185	rs428957	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52843131	rs367836	G	T	2227.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=54;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.34;SOR=8.015;VQSLOD=7.12;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2256,163,0
-chr6	52843477	rs375887	A	G	995.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=26;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.28;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.52;SOR=5.058;VQSLOD=6.33;culprit=FS;GENE=GSTA4,RNY3P15	GT:AD:DP:GQ:PL	1/1:0,25:25:75:1024,75,0
-chr6	52843524	rs543613	T	C	344.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.54;SOR=4.615;VQSLOD=4.87;culprit=FS;GENE=GSTA4,RNY3P15	GT:AD:DP:GQ:PL	1/1:0,9:9:27:373,27,0
-chr6	52847150	rs67390777	TA	T	38.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=66.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=12.75;SOR=2.833;VQSLOD=8.55;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,3:3:9:75,9,0
-chr6	52847273	rs3831189	T	TAC	756.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.167;ClippingRankSum=0.026;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.26;MQ0=0;MQRankSum=-0.078;POSITIVE_TRAIN_SITE;QD=22.93;ReadPosRankSum=0.544;SOR=2.621;VQSLOD=6.58;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	0/1:6,24:30:99:794,0,101
-chr6	52847551	rs316133	G	C	3193.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=83;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.28;SOR=2.833;VQSLOD=6.64;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,83:83:99:3222,249,0
-chr6	52847682	rs10557482	GGAGA	G	232.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=62.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=3.912;VQSLOD=6.22;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,6:6:18:270,18,0
-chr6	52849146	rs316128	G	T	959.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=28;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.28;SOR=5.136;VQSLOD=6.09;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,26:26:78:988,78,0
-chr6	52849481	.	C	CT	353.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.178;ClippingRankSum=-1.73;DP=59;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.53;MQ0=0;MQRankSum=-0.663;POSITIVE_TRAIN_SITE;QD=6.0;ReadPosRankSum=-1.275;SOR=1.609;VQSLOD=5.78;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	0/1:14,23:37:99:391,0,172
-chr6	52850040	rs669674	A	G	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.43;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	52851936	rs508078	T	C	1473.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=38;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.45;SOR=5.031;VQSLOD=7.06;culprit=FS;GENE=GSTA4	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1502,114,0
-chr6	52881235	rs11756408	C	T	143.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.198;POSITIVE_TRAIN_SITE;QD=20.54;ReadPosRankSum=-0.922;SOR=1.609;VQSLOD=5.81;culprit=FS;GENE=ICK	GT:AD:DP:GQ:PL	0/1:2,5:7:63:172,0,63
-chr6	52892683	rs222456	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ICK	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52929010	rs11401639	A	AT	12.93	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.47;SOR=0.693;GENE=FBXO9	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52938468	.	AT	A	1342.73	PASS	AC=2;AF=1.0;AN=2;BaseQRankSum=-0.585;ClippingRankSum=-0.022;DP=99;FS=6.337;MLEAC=2;MLEAF=1.0;MQ=60.68;MQ0=0;MQRankSum=-0.412;POSITIVE_TRAIN_SITE;QD=13.56;ReadPosRankSum=-1.299;SOR=3.952;VQSLOD=1.47;culprit=FS;GENE=FBXO9	GT:AD:DP:GQ:PL	1/1:2,62:64:99:1380,141,0
-chr6	52941597	rs34970749	TA	T	32.71	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.35;SOR=0.693;VQSLOD=7.09;culprit=FS;GENE=FBXO9	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	52943841	rs35757290	TA	T	559.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=18;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.53;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.1;SOR=5.67;VQSLOD=5.92;culprit=FS;GENE=FBXO9	GT:AD:DP:GQ:PL	1/1:0,16:16:48:597,48,0
-chr6	52958479	rs2816350	A	G	1666.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=45;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.21;SOR=3.816;VQSLOD=6.04;culprit=FS;GENE=FBXO9	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1695,132,0
-chr6	52962715	rs2744455	C	T	1715.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=44;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.2;SOR=6.184;VQSLOD=5.9;culprit=FS;GENE=FBXO9	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1744,132,0
-chr6	52985368	rs6919768	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52992851	rs377590473	AGAAGG	A	35.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.663;ClippingRankSum=1.055;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.25;MQ0=0;MQRankSum=-2.362;QD=1.7;ReadPosRankSum=0.28;SOR=0.043;VQSLOD=3.98;culprit=FS;GENE=GCM1	GT:AD:DP:GQ:PL	0/1:18,3:21:73:73,0,1155
-chr6	52998788	rs2816346	G	A	128.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.97;culprit=FS;GENE=GCM1	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-chr6	52998834	rs2816345	C	T	125.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.247;ClippingRankSum=-0.163;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-0.054;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.464;SOR=0.307;VQSLOD=5.43;culprit=QD;GENE=GCM1	GT:AD:DP:GQ:PL	0/1:10,6:16:99:154,0,317
-chr6	52998856	rs2518573	T	G	225.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.191;ClippingRankSum=0.439;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.13;MQ0=0;MQRankSum=-0.322;POSITIVE_TRAIN_SITE;QD=9.03;ReadPosRankSum=-0.966;SOR=0.412;VQSLOD=4.85;culprit=FS;GENE=GCM1	GT:AD:DP:GQ:PL	0/1:14,10:24:99:254,0,473
-chr6	53010182	rs9367511	A	G	116.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.927;ClippingRankSum=-0.533;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.212;POSITIVE_TRAIN_SITE;QD=8.98;ReadPosRankSum=1.092;SOR=0.368;VQSLOD=5.93;culprit=FS;GENE=GCM1	GT:AD:DP:GQ:PL	0/1:8,5:13:99:145,0,291
-chr6	53010609	rs59049517	TA	T	57.9	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.731;ClippingRankSum=0.731;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.53;MQ0=0;MQRankSum=-0.731;POSITIVE_TRAIN_SITE;QD=8.27;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.42;culprit=FS;GENE=GCM1	GT:AD:DP:GQ:PL	0/1:1,4:5:14:95,0,14
-chr6	53061391	rs78303998	G	A	114.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.017;ClippingRankSum=-0.421;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.922;QD=14.35;ReadPosRankSum=0.421;SOR=0.693;VQSLOD=4.6;culprit=FS;GENE=SOD1P1	GT:AD:DP:GQ:PL	0/1:4,4:8:99:143,0,121
-chr6	53062469	rs7772870	G	A	98.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=1.179;VQSLOD=7.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:126,9,0
-chr6	53071745	rs77744774	C	T	100.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.48;ClippingRankSum=-1.271;DB;DP=10;FS=6.99;MLEAC=1;MLEAF=0.5;MQ=41.67;MQ0=0;MQRankSum=-1.733;QD=10.08;ReadPosRankSum=0.0;SOR=4.407;VQSLOD=-0.7559;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,8:10:38:129,0,38
-chr6	53072388	rs62413047	A	C	120.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.447;ClippingRankSum=-0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.036;POSITIVE_TRAIN_SITE;QD=12.08;ReadPosRankSum=1.133;SOR=1.329;VQSLOD=4.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,6:10:99:149,0,125
-chr6	53072441	rs11758224	A	G	29.77	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.067;ClippingRankSum=-1.067;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.572;QD=3.72;ReadPosRankSum=-1.067;SOR=0.693	GT:AD:DP:GQ:PL	0/1:6,2:8:58:58,0,221
-chr6	53072501	rs11756086	T	C	22.79	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-1.495;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.198;QD=3.26;ReadPosRankSum=-0.198;SOR=1.802	GT:AD:DP:GQ:PL	0/1:5,2:7:51:51,0,184
-chr6	53103062	rs10583094	TAC	T	36.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.35;SOR=0.693;VQSLOD=8.72;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	53119938	.	G	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	53120011	.	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53173704	rs209484	C	T	29.79	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=9.93;ReadPosRankSum=-0.736;SOR=0.223;GENE=ELOVL5	GT:AD:DP:GQ:PL	0/1:1,2:3:25:58,0,25
-chr6	53186203	rs209499	C	T	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.79;culprit=FS;GENE=ELOVL5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	53210951	rs209523	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ELOVL5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53229240	rs1346602	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	53302223	rs11967914	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53306308	rs1401156	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53325093	rs11969450	G	A	33.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:34:62,0,34
-chr6	53363487	rs10604357	GGGCT	G	931.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.719;ClippingRankSum=0.942;DB;DP=65;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.9;MQ0=0;MQRankSum=-0.356;POSITIVE_TRAIN_SITE;QD=14.33;ReadPosRankSum=0.364;SOR=1.141;VQSLOD=6.29;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:37,26:63:99:969,0,1920
-chr6	53365019	rs661346	G	C	4389.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=126;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.84;SOR=1.262;VQSLOD=6.97;culprit=QD;GENE=GCLC	GT:AD:DP:GQ:PL	1/1:0,125:125:99:4418,375,0
-chr6	53366008	rs12525473	C	T	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.18;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	53366061	rs12525474	C	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.08;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	53370107	rs661603	T	C	253.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.678;ClippingRankSum=0.998;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.103;POSITIVE_TRAIN_SITE;QD=15.86;ReadPosRankSum=-0.578;SOR=0.693;VQSLOD=6.35;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:8,8:16:99:282,0,260
-chr6	53370327	rs17884019	C	T	446.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.961;ClippingRankSum=-0.471;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.3;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=0.848;SOR=1.112;VQSLOD=4.7;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:16,16:32:99:475,0,461
-chr6	53372145	rs1555903	T	C	760.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.717;ClippingRankSum=-1.83;DB;DP=57;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.171;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=0.024;SOR=0.385;VQSLOD=5.78;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:34,23:57:99:789,0,1142
-chr6	53373197	rs2235707	G	C	375.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.581;ClippingRankSum=-1.193;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.25;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=0.028;SOR=0.387;VQSLOD=5.68;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:15,10:25:99:404,0,860
-chr6	53373198	rs17880319	A	G	375.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.38;ClippingRankSum=-0.765;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.716;SOR=0.404;VQSLOD=4.81;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:16,11:27:99:404,0,860
-chr6	53373276	rs17881410	C	T	1348.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.532;ClippingRankSum=-1.183;DB;DP=82;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.72;MQ0=0;MQRankSum=0.107;POSITIVE_TRAIN_SITE;QD=16.45;ReadPosRankSum=0.654;SOR=0.742;VQSLOD=4.98;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:40,42:82:99:1377,0,1369
-chr6	53373624	rs3830795	G	GCTCCAC	706.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.129;ClippingRankSum=-1.149;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.77;MQ0=0;MQRankSum=-5.319;POSITIVE_TRAIN_SITE;QD=14.13;ReadPosRankSum=-0.966;SOR=0.399;VQSLOD=1.11;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:29,20:49:99:744,0,1894
-chr6	53378861	rs11385177	A	AT	433.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.124;ClippingRankSum=-1.535;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.249;POSITIVE_TRAIN_SITE;QD=14.46;ReadPosRankSum=0.456;SOR=0.693;VQSLOD=6.6;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:15,15:30:99:471,0,469
-chr6	53379193	rs17885705	A	T	3122.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.101;ClippingRankSum=-0.402;DB;DP=206;FS=0.54;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.173;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.72;SOR=0.781;VQSLOD=1.97;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:103,103:206:99:3151,0,3088
-chr6	53379352	rs17881444	A	G	1554.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.383;ClippingRankSum=1.328;DB;DP=104;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=14.95;ReadPosRankSum=1.368;SOR=0.719;VQSLOD=3.93;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:55,49:104:99:1583,0,1676
-chr6	53379405	rs3736729	A	C	1019.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.536;ClippingRankSum=0.059;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.059;POSITIVE_TRAIN_SITE;QD=20.4;ReadPosRankSum=-1.69;SOR=1.051;VQSLOD=4.96;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:21,29:50:99:1048,0,693
-chr6	53379499	rs17883806	G	C	182.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.133;ClippingRankSum=-2.383;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.866;POSITIVE_TRAIN_SITE;QD=18.28;ReadPosRankSum=-0.741;SOR=1.085;VQSLOD=5.36;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:4,6:10:99:211,0,139
-chr6	53385934	rs17883816	T	C	291.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.062;ClippingRankSum=0.766;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.237;POSITIVE_TRAIN_SITE;QD=19.45;ReadPosRankSum=1.591;SOR=1.112;VQSLOD=4.79;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:6,9:15:99:320,0,184
-chr6	53394065	rs17883125	C	T	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=7.91;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	53409451	.	C	CCCT	53.7	PASS	AC=2;AF=1.0;AN=2;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=13.43;SOR=2.303;VQSLOD=6.3;culprit=FS;GENE=GCLC	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	53470507	rs9349679	G	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=GCLC	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	53493640	rs6925537	T	C	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.13;SOR=1.609;VQSLOD=6.84;culprit=FS;GENE=LINC01564	GT:AD:DP:GQ:PL	1/1:0,1:1:6:83,6,0
-chr6	53493642	rs6903184	G	C	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.55;culprit=FS;GENE=LINC01564	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	53516876	rs6928338	T	G	250.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=38.13;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.86;SOR=0.892;VQSLOD=6.06;culprit=FS;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,9:9:27:279,27,0
-chr6	53519062	rs10948758	A	G	5150.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=125;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.87;SOR=0.882;VQSLOD=6.17;culprit=FS;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,125:125:99:5179,376,0
-chr6	53519605	rs3799260	C	T	7091.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=190;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.76;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.12;SOR=0.693;VQSLOD=2.98;culprit=FS;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,190:190:99:7120,571,0
-chr6	53519857	rs12210809	G	A	4207.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=112;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=36.51;SOR=1.22;VQSLOD=5.94;culprit=QD;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,110:110:99:4236,331,0
-chr6	53520088	rs2038939	T	C	2813.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.28;SOR=3.643;VQSLOD=5.42;culprit=FS;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2842,207,0
-chr6	53520124	rs2038940	A	G	1799.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=46;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.5;MQ0=0;QD=29.97;SOR=6.273;VQSLOD=4.73;culprit=FS;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1828,138,0
-chr6	53528784	rs1326553	A	G	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.43;culprit=FS;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	53529027	rs1326554	A	T	3242.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=87;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=37.3;SOR=4.929;VQSLOD=5.98;culprit=QD;GENE=KLHL31	GT:AD:DP:GQ:PL	1/1:0,87:87:99:3271,262,0
-chr6	53543213	rs4541744	C	T	99.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=1.179;VQSLOD=7.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:127,9,0
-chr6	53559094	rs10452610	A	G	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	53586617	rs35610624	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53601883	rs7745277	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53606394	rs4457161	T	C	12.07	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:23:40,0,23
-chr6	53620789	rs7763482	C	T	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=2.303;VQSLOD=9.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	53626319	.	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53654033	rs3001010	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	53662935	rs9382237	C	T	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=6.56;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	53674284	rs4475321	C	T	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.61;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	53676354	rs4715425	G	A	91.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=7.98;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	53690779	rs3003489	T	C	46.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.83;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	53691835	rs7755924	A	G	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.14;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	53694407	rs6904545	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53707098	rs4286781	C	T	4179.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=110;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.61;SOR=2.876;VQSLOD=6.95;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,110:110:99:4208,331,0
-chr6	53723062	rs145334901	AT	A	13.89	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.94;SOR=2.303;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:50,6,0
-chr6	53726761	rs3935663	C	T	47.79	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.71;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:1,2:3:22:76,0,22
-chr6	53726780	rs3935664	A	G	90.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=1.179;VQSLOD=9.22;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:118,9,0
-chr6	53749074	rs4265034	G	C	79.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.43;SOR=2.833;VQSLOD=8.11;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:107,9,0
-chr6	53755300	rs6458972	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53762210	rs62397108	C	A	270.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.681;ClippingRankSum=-0.033;DB;DP=23;FS=4.904;MLEAC=1;MLEAF=0.5;MQ=59.19;MQ0=0;MQRankSum=0.824;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.89;SOR=2.165;VQSLOD=2.61;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:12,10:22:99:299,0,376
-chr6	53764829	rs71558840	T	G	125.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.804;ClippingRankSum=1.304;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=39.8;MQ0=0;MQRankSum=2.136;QD=4.84;ReadPosRankSum=1.969;SOR=0.387;VQSLOD=1.71;culprit=QD;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:15,10:25:99:154,0,298
-chr6	53778661	rs201915048	T	G	38.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.938;ClippingRankSum=-0.459;DB;DP=84;FS=136.465;MLEAC=1;MLEAF=0.5;MQ=49.9;MQ0=0;MQRankSum=-5.277;QD=0.46;ReadPosRankSum=-6.784;SOR=6.271;VQSLOD=-42.91;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:61,22:83:67:67,0,1974
-chr6	53784268	rs59246960	C	CT	332.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=17;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.32;MQ0=0;QD=19.57;SOR=5.549;VQSLOD=4.44;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	1/1:0,15:15:45:370,45,0
-chr6	53784662	rs3777661	A	G	109.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.0;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.47;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:4,4:8:99:138,0,134
-chr6	53785276	rs2294789	C	A	178.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.383;ClippingRankSum=-0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=17.88;ReadPosRankSum=-2.072;SOR=1.085;VQSLOD=5.18;culprit=ReadPosRankSum;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:4,6:10:99:207,0,141
-chr6	53785759	rs201940946	G	GT	45.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.55;ClippingRankSum=-0.55;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.34;MQ0=0;MQRankSum=-0.55;QD=5.72;ReadPosRankSum=-0.937;SOR=0.941;VQSLOD=4.79;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:3,4:7:54:83,0,54
-chr6	53787267	rs2294791	G	C	221.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.074;ClippingRankSum=1.656;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.935;POSITIVE_TRAIN_SITE;QD=17.06;ReadPosRankSum=0.101;SOR=0.836;VQSLOD=6.75;culprit=FS;GENE=LRRC1	GT:AD:DP:GQ:PL	0/1:6,7:13:99:250,0,220
-chr6	53805460	rs6907354	A	G	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.61;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	53893735	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53927326	rs4715439	T	C	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.26;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	53953083	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53973251	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53982990	rs4521576	A	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.14;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	53986503	rs2145754	A	T	180.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.749;ClippingRankSum=1.186;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.466;POSITIVE_TRAIN_SITE;QD=16.43;ReadPosRankSum=1.932;SOR=0.859;VQSLOD=6.2;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:5,6:11:99:209,0,162
-chr6	53989526	rs4712056	G	A	2189.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.153;ClippingRankSum=1.695;DB;DP=131;FS=6.808;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-1.076;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=1.657;SOR=0.326;VQSLOD=1.81;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:59,70:129:99:2218,0,1820
-chr6	54003899	rs11965480	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.24;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	54013765	rs2145755	A	G	923.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.107;ClippingRankSum=0.838;DB;DP=48;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.142;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=0.735;SOR=0.866;VQSLOD=4.39;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:22,26:48:99:952,0,728
-chr6	54025155	rs10484648	T	C	760.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.724;ClippingRankSum=0.655;DB;DP=56;FS=1.455;MLEAC=1;MLEAF=0.5;MQ=59.59;MQ0=0;MQRankSum=-0.099;POSITIVE_TRAIN_SITE;QD=13.59;ReadPosRankSum=0.458;SOR=1.151;VQSLOD=3.37;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:30,23:53:99:789,0,990
-chr6	54030072	rs1280860	T	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.53;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	54035531	rs2792626	T	C	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=9.15;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	54046086	rs2792632	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54054686	rs6934690	T	A	2471.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.306;ClippingRankSum=-2.348;DB;DP=167;FS=1.953;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=14.8;ReadPosRankSum=1.55;SOR=0.892;VQSLOD=2.86;culprit=DP;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:79,88:167:99:2500,0,2110
-chr6	54054837	rs9296739	A	G	811.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.037;ClippingRankSum=-2.468;DB;DP=45;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.876;POSITIVE_TRAIN_SITE;QD=18.04;ReadPosRankSum=-1.149;SOR=0.829;VQSLOD=5.35;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:21,24:45:99:840,0,675
-chr6	54058426	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54067088	rs67016420	AT	A	245.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.88;ClippingRankSum=-0.81;DB;DP=24;FS=3.222;MLEAC=1;MLEAF=0.5;MQ=62.65;MQ0=0;MQRankSum=1.303;POSITIVE_TRAIN_SITE;QD=10.24;ReadPosRankSum=0.88;SOR=0.16;VQSLOD=2.56;culprit=MQRankSum;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:11,10:21:99:283,0,313
-chr6	54095411	rs2275770	C	G	1855.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.478;ClippingRankSum=-0.434;DB;DP=111;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.74;MQ0=0;MQRankSum=1.03;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=-1.101;SOR=0.609;VQSLOD=4.2;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:58,53:111:99:1884,0,2350
-chr6	54095423	rs816384	T	C	2503.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=6.058;ClippingRankSum=-0.087;DB;DP=130;FS=7.052;MLEAC=1;MLEAF=0.5;MQ=58.75;MQ0=0;MQRankSum=-0.073;POSITIVE_TRAIN_SITE;QD=19.26;ReadPosRankSum=0.105;SOR=2.758;VQSLOD=0.745;culprit=FS;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:58,72:130:99:2532,0,2153
-chr6	54095524	rs2275769	C	T	4212.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.148;ClippingRankSum=1.384;DB;DP=307;FS=2.75;MLEAC=1;MLEAF=0.5;MQ=59.09;MQ0=0;MQRankSum=-1.33;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=0.874;SOR=0.887;VQSLOD=1.41;culprit=DP;GENE=MLIP	GT:AD:DP:GQ:PL	0/1:165,138:303:99:4241,0,5117
-chr6	54157748	rs6458990	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54157803	rs149997923	G	GTT	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54157804	rs13211037	A	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54159866	rs7775058	C	T	83.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.76;SOR=1.179;VQSLOD=7.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:111,9,0
-chr6	54159915	rs7740868	G	T	64.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=2.833;VQSLOD=8.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	54166206	.	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54166208	.	CA	C	43.79	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=14.6;SOR=0.223;VQSLOD=4.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:19:81,0,19
-chr6	54173085	rs2297981	T	A	239.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.26;SOR=4.174;VQSLOD=7.06;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,7:7:21:268,21,0
-chr6	54175705	rs148816365	C	CTTTCTT	143	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=34.37;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.01;SOR=1.609;VQSLOD=8.24;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,4:4:12:180,12,0
-chr6	54185689	rs2297983	G	T	92.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=2.833;VQSLOD=9.04;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,3:3:9:120,9,0
-chr6	54186024	rs2297986	T	C	1611.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=43;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.67;SOR=5.235;VQSLOD=7.3;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1640,126,0
-chr6	54186147	rs1058768	T	C	3340.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=91;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.94;SOR=0.906;VQSLOD=4.55;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3369,274,0
-chr6	54191363	rs9370289	G	A	180.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.611;VQSLOD=5.85;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,5:5:15:209,15,0
-chr6	54191970	rs1848440	T	A	4352.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=121;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.31;SOR=3.556;VQSLOD=5.9;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,121:121:99:4381,364,0
-chr6	54208353	rs1417387	T	C	185.84	PASS	AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.97;SOR=3.912;VQSLOD=6.78;culprit=FS;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,6:6:18:214,18,0
-chr6	54212964	rs1876606	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=TINAG	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54349833	rs2294725	G	A	95.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.017;ClippingRankSum=0.0;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=43.31;MQ0=0;MQRankSum=0.421;POSITIVE_TRAIN_SITE;QD=11.97;ReadPosRankSum=-1.368;SOR=0.693;VQSLOD=5.69;culprit=FS;GENE=CLNS1AP1	GT:AD:DP:GQ:PL	0/1:4,4:8:99:124,0,121
-chr6	54350048	rs807991	G	A	997.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.754;ClippingRankSum=0.019;DB;DP=73;FS=12.208;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.551;SOR=0.108;VQSLOD=1.6;culprit=FS;GENE=CLNS1AP1	GT:AD:DP:GQ:PL	0/1:28,38:66:99:1026,0,963
-chr6	54350422	rs565623	G	A	1056.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.722;ClippingRankSum=-0.634;DB;DP=67;FS=3.327;MLEAC=1;MLEAF=0.5;MQ=59.66;MQ0=0;MQRankSum=0.433;POSITIVE_TRAIN_SITE;QD=15.77;ReadPosRankSum=-1.01;SOR=1.142;VQSLOD=2.92;culprit=ReadPosRankSum;GENE=CLNS1AP1	GT:AD:DP:GQ:PL	0/1:32,35:67:99:1085,0,982
-chr6	54356832	rs3900305	T	A	31.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=6.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=5.26;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,2:5:60:60,0,75
-chr6	54438922	rs10447409	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54467267	rs1951694	A	G	44.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.23;culprit=FS;GENE=RPL10P10	GT:AD:DP:GQ:PL	0/1:1,2:3:32:73,0,32
-chr6	54477874	rs5876389	T	TA	16.8	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=8.4;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:53,6,0
-chr6	54485844	rs7766941	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54489986	rs10948830	G	A	2797.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.226;ClippingRankSum=-0.973;DB;DP=129;FS=4.335;MLEAC=1;MLEAF=0.5;MQ=59.28;MQ0=0;MQRankSum=1.3;NEGATIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=1.119;SOR=0.983;VQSLOD=-1.343;culprit=DP;GENE=RPSAP44	GT:AD:DP:GQ:PL	0/1:54,73:127:99:2826,0,2602
-chr6	54489990	rs10948831	A	G	2774.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.682;ClippingRankSum=-0.704;DB;DP=125;FS=2.332;MLEAC=1;MLEAF=0.5;MQ=59.26;MQ0=0;MQRankSum=0.479;POSITIVE_TRAIN_SITE;QD=22.2;ReadPosRankSum=0.468;SOR=0.927;VQSLOD=0.604;culprit=DP;GENE=RPSAP44	GT:AD:DP:GQ:PL	0/1:52,71:123:99:2803,0,2545
-chr6	54490041	rs9349726	T	C	2720.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.83;ClippingRankSum=-0.591;DB;DP=155;FS=2.034;MLEAC=1;MLEAF=0.5;MQ=58.04;MQ0=0;MQRankSum=2.054;POSITIVE_TRAIN_SITE;QD=17.55;ReadPosRankSum=0.525;SOR=0.513;VQSLOD=1.47;culprit=MQRankSum;GENE=RPSAP44	GT:AD:DP:GQ:PL	0/1:71,82:153:99:2749,0,2148
-chr6	54490338	rs10807475	T	A	832.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.069;ClippingRankSum=-0.537;DB;DP=81;FS=11.744;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.204;POSITIVE_TRAIN_SITE;QD=10.28;ReadPosRankSum=0.105;SOR=0.051;VQSLOD=0.328;culprit=FS;GENE=RPSAP44	GT:AD:DP:GQ:PL	0/1:36,38:74:99:870,0,1117
-chr6	54500405	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54557514	rs1395632	G	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	54571089	rs6907631	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54635275	rs2397171	G	C	38.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=-0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.72;POSITIVE_TRAIN_SITE;QD=6.46;ReadPosRankSum=0.72;SOR=0.307;VQSLOD=5.95;culprit=QD;GENE=KRASP1	GT:AD:DP:GQ:PL	0/1:4,2:6:67:67,0,148
-chr6	54635398	rs5876400	T	TG	256.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.6;ClippingRankSum=-2.0;DB;DP=14;FS=2.363;MLEAC=1;MLEAF=0.5;MQ=51.87;MQ0=0;MQRankSum=-1.733;POSITIVE_TRAIN_SITE;QD=18.34;ReadPosRankSum=-1.467;SOR=1.288;VQSLOD=1.73;culprit=MQRankSum;GENE=KRASP1	GT:AD:DP:GQ:PL	0/1:5,9:14:99:294,0,145
-chr6	54635417	rs4516942	G	A	237.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.532;ClippingRankSum=-0.794;DB;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.69;MQ0=0;MQRankSum=-1.172;POSITIVE_TRAIN_SITE;QD=11.89;ReadPosRankSum=-0.189;SOR=0.693;VQSLOD=4.98;culprit=FS;GENE=KRASP1	GT:AD:DP:GQ:PL	0/1:10,10:20:99:266,0,354
-chr6	54635605	rs73742825	C	G	103.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.07;MQ0=0;QD=17.17;SOR=1.609;VQSLOD=3.97;culprit=FS;GENE=KRASP1	GT:AD:DP:GQ:PL	1/1:0,4:4:12:131,12,0
-chr6	54661634	rs12216186	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	54672835	rs10807480	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54682692	.	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54691959	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54692294	rs72957572	A	G	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	54734941	rs7765721	C	A	557.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.038;ClippingRankSum=-1.807;DB;DP=46;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.5;MQ0=0;MQRankSum=0.312;POSITIVE_TRAIN_SITE;QD=12.13;ReadPosRankSum=0.089;SOR=0.412;VQSLOD=4.55;culprit=FS;GENE=FAM83B	GT:AD:DP:GQ:PL	0/1:27,19:46:99:586,0,962
-chr6	54735122	rs1472679	A	G	2623.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.37;ClippingRankSum=-0.594;DB;DP=179;FS=1.203;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=-0.157;POSITIVE_TRAIN_SITE;QD=14.66;ReadPosRankSum=1.205;SOR=0.798;VQSLOD=2.83;culprit=DP;GENE=FAM83B	GT:AD:DP:GQ:PL	0/1:91,86:177:99:2652,0,2889
-chr6	54735594	rs995851	G	A	418.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.928;ClippingRankSum=0.395;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.187;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=-0.686;SOR=0.576;VQSLOD=5.25;culprit=ReadPosRankSum;GENE=FAM83B	GT:AD:DP:GQ:PL	0/1:16,14:30:99:447,0,581
-chr6	54735606	rs995852	G	A	893.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=23;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.18;SOR=6.358;VQSLOD=6.01;culprit=FS;GENE=FAM83B	GT:AD:DP:GQ:PL	1/1:0,23:23:69:922,69,0
-chr6	54792553	.	G	A	1230.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.237;ClippingRankSum=1.275;DP=82;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=36.68;MQ0=0;MQRankSum=-1.187;QD=15.01;ReadPosRankSum=-0.624;SOR=1.402;VQSLOD=3.32;culprit=FS;GENE=FAM83B	GT:AD:DP:GQ:PL	0/1:27,48:75:99:1259,0,685
-chr6	54807006	rs171224	T	G	114.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.638;ClippingRankSum=1.368;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=14.35;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.54;culprit=FS;GENE=FAM83B	GT:AD:DP:GQ:PL	0/1:4,4:8:99:143,0,127
-chr6	54824610	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54857680	rs2134536	G	A	45.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=0.988;SOR=0.693;VQSLOD=5.75;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,3:6:73:74,0,73
-chr6	54936685	rs57552002	T	TAATA	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54938529	rs4312988	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54998074	rs9370385	A	G	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.03;culprit=FS;GENE=HCRTR2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	55003132	rs9349759	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=HCRTR2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55028053	rs200898132	CAACA	C	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=50.6;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=6.89;culprit=FS;GENE=HCRTR2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	55028113	rs6459069	C	T	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=50.6;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.01;culprit=FS;GENE=HCRTR2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	55040774	rs4615392	A	G	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=8.67;culprit=FS;GENE=HCRTR2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	55045025	rs9370399	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=HCRTR2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55113411	rs3122169	C	A	2001.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.942;ClippingRankSum=-1.093;DB;DP=131;FS=4.929;MLEAC=1;MLEAF=0.5;MQ=59.47;MQ0=0;MQRankSum=-0.196;POSITIVE_TRAIN_SITE;QD=15.28;ReadPosRankSum=-0.937;SOR=1.302;VQSLOD=2.09;culprit=DP;GENE=HCRTR2	GT:AD:DP:GQ:PL	0/1:65,66:131:99:2030,0,2129
-chr6	55142337	rs2653349	A	G	920.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.329;ClippingRankSum=-0.235;DB;DP=82;FS=3.142;MLEAC=1;MLEAF=0.5;MQ=57.13;MQ0=0;MQRankSum=0.602;POSITIVE_TRAIN_SITE;QD=11.23;ReadPosRankSum=1.94;SOR=1.11;VQSLOD=2.51;culprit=ReadPosRankSum;GENE=HCRTR2	GT:AD:DP:GQ:PL	0/1:47,31:78:99:949,0,1545
-chr6	55142458	rs11455646	C	CT	65.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.309;ClippingRankSum=-1.788;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.78;MQ0=0;MQRankSum=0.244;POSITIVE_TRAIN_SITE;QD=2.99;ReadPosRankSum=-0.38;SOR=0.446;VQSLOD=6.64;culprit=FS;GENE=HCRTR2	GT:AD:DP:GQ:PL	0/1:7,7:14:99:103,0,107
-chr6	55190480	rs12110721	G	A	59.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.76;SOR=1.179;VQSLOD=7.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:87,9,0
-chr6	55196299	rs4715531	C	A	87.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=2.833;VQSLOD=9.04;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,3:3:9:115,9,0
-chr6	55196587	rs12199003	C	T	2169.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.778;ClippingRankSum=1.972;DB;DP=139;FS=4.029;MLEAC=1;MLEAF=0.5;MQ=59.87;MQ0=0;MQRankSum=-0.737;POSITIVE_TRAIN_SITE;QD=15.61;ReadPosRankSum=1.585;SOR=0.438;VQSLOD=2.24;culprit=DP;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:67,71:138:99:2198,0,1867
-chr6	55206112	rs7761953	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55215079	rs1032767	G	A	1033.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.33;SOR=5.211;VQSLOD=6.59;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,27:27:81:1062,81,0
-chr6	55215155	rs7743512	C	T	247.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.106;ClippingRankSum=1.059;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.106;POSITIVE_TRAIN_SITE;QD=15.49;ReadPosRankSum=-1.164;SOR=0.976;VQSLOD=5.41;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:7,9:16:99:276,0,215
-chr6	55216005	rs870806	G	A	1207.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.265;ClippingRankSum=0.451;DB;DP=75;FS=2.105;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.005;POSITIVE_TRAIN_SITE;QD=16.1;ReadPosRankSum=0.589;SOR=0.234;VQSLOD=3.38;culprit=DP;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:36,39:75:99:1236,0,1296
-chr6	55223501	rs41474045	T	G	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.2;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	55223531	rs62419074	A	G	95.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.763;ClippingRankSum=1.11;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.457;POSITIVE_TRAIN_SITE;QD=6.38;ReadPosRankSum=0.457;SOR=0.16;VQSLOD=4.75;culprit=QD;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:11,4:15:99:124,0,384
-chr6	55223962	.	G	GTCTATCTATCTATCTA	839.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.176;ClippingRankSum=1.806;DP=80;FS=1.944;MLEAC=1;MLEAF=0.5;MQ=57.42;MQ0=0;MQRankSum=-1.121;POSITIVE_TRAIN_SITE;QD=10.5;ReadPosRankSum=-2.584;SOR=0.237;VQSLOD=1.23;culprit=ReadPosRankSum;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:30,22:52:99:877,0,3184
-chr6	55224107	rs9475257	A	G	80.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.231;POSITIVE_TRAIN_SITE;QD=16.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=5.3;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:2,3:5:65:109,0,65
-chr6	55227565	rs17830060	T	C	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.57;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	55227593	rs9475263	C	T	30.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.72;ClippingRankSum=0.0;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=1.38;POSITIVE_TRAIN_SITE;QD=5.13;ReadPosRankSum=-0.72;SOR=1.179;VQSLOD=5.45;culprit=QD;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:4,2:6:59:59,0,110
-chr6	55227683	rs9475264	C	G	70.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.248;ClippingRankSum=-0.248;DB;DP=9;FS=3.01;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.573;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.203;SOR=1.911;VQSLOD=1.76;culprit=QD;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:6,3:9:99:99,0,193
-chr6	55227930	rs35444148	CA	C	43.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.42;SOR=2.833;VQSLOD=8.08;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,3:3:9:80,9,0
-chr6	55258643	rs28479599	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55263789	rs9396088	C	T	128.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.51;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-chr6	55263921	rs41271314	T	C	376.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.406;ClippingRankSum=0.798;DB;DP=32;FS=4.26;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.044;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.136;SOR=0.078;VQSLOD=2.13;culprit=MQRankSum;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:20,12:32:99:405,0,694
-chr6	55264362	rs6936510	T	C	1182.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=28;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.65;SOR=6.736;VQSLOD=6.62;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,28:28:84:1211,84,0
-chr6	55264461	rs6913781	C	T	236.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.83;SOR=4.174;VQSLOD=6.61;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,7:7:21:265,21,0
-chr6	55266394	rs1546297	T	A	509.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.23;SOR=5.283;VQSLOD=7.14;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,13:13:39:538,39,0
-chr6	55266625	rs9370418	T	C	5961.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=169;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.73;SOR=1.061;VQSLOD=5.15;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,169:169:99:5990,508,0
-chr6	55266722	rs12529201	C	T	2018.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=54;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.58;SOR=6.593;VQSLOD=6.37;culprit=FS;GENE=GFRAL	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2047,162,0
-chr6	55266796	rs10948913	C	T	23.79	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.48;QD=2.38;ReadPosRankSum=1.271;SOR=0.105;GENE=GFRAL	GT:AD:DP:GQ:PL	0/1:8,2:10:52:52,0,252
-chr6	55275656	rs884360	A	C	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	55294300	rs1393326	T	A	60.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=7.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	55297178	rs1032766	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55334381	rs9382495	G	A	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.86;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	55357373	rs4530860	A	G	71.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=6.89;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	55358360	rs9475318	A	G	91.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=8.42;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	55359142	rs70986720	A	AC	44.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.16;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	55359361	rs62407080	T	A	121.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.467;ClippingRankSum=0.267;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.2;POSITIVE_TRAIN_SITE;QD=8.7;ReadPosRankSum=1.067;SOR=0.307;VQSLOD=4.49;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	0/1:9,5:14:99:150,0,312
-chr6	55360086	rs4538708	A	G	530.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=5.283;VQSLOD=7.04;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,13:13:39:559,39,0
-chr6	55361878	rs9475319	T	C	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=9.03;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	55365910	rs59233169	A	ACT	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.75;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	55368931	rs4540264	T	C	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.52;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	55378633	rs13206666	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.78;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	55381262	rs6459082	G	A	5521.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=145;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.7;SOR=4.22;VQSLOD=6.17;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,145:145:99:5550,436,0
-chr6	55381574	rs9464253	T	G	460.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.44;SOR=5.283;VQSLOD=7.38;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,13:13:39:489,39,0
-chr6	55381594	rs9464254	T	C	300.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.19;SOR=4.407;VQSLOD=7.05;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,8:8:24:329,24,0
-chr6	55392955	rs7743010	C	G	87.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.13;SOR=0.693;VQSLOD=8.45;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:9:115,9,0
-chr6	55392956	rs7743274	G	A	87.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=1.179;VQSLOD=7.93;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:115,9,0
-chr6	55406399	rs9367638	C	T	1374.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=36;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.41;SOR=7.223;VQSLOD=6.72;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1403,108,0
-chr6	55425387	rs9367641	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55431875	rs9464265	C	G	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.15;culprit=FS;GENE=HMGCLL1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	55471178	rs4583976	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55494744	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55509428	rs4504466	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55519639	rs10807498	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55545792	rs34899952	C	T	572.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=15;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.12;SOR=5.549;VQSLOD=6.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,15:15:45:601,45,0
-chr6	55625041	rs3798845	G	A	44.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.67;culprit=FS;GENE=BMP5	GT:AD:DP:GQ:PL	0/1:1,2:3:26:73,0,26
-chr6	55714314	rs62404968	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=BMP5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55730212	rs2021803	G	A	169.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.969;ClippingRankSum=-0.648;DB;DP=22;FS=1.707;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.126;POSITIVE_TRAIN_SITE;QD=7.72;ReadPosRankSum=1.126;SOR=1.179;VQSLOD=2.48;culprit=QD;GENE=BMP5	GT:AD:DP:GQ:PL	0/1:14,8:22:99:198,0,496
-chr6	55739553	rs3734444	A	G	5242.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=7.927;ClippingRankSum=0.832;DB;DP=341;FS=2.501;MLEAC=1;MLEAF=0.5;MQ=59.13;MQ0=0;MQRankSum=1.703;POSITIVE_TRAIN_SITE;QD=15.37;ReadPosRankSum=0.746;SOR=0.848;VQSLOD=1.42;culprit=DP;GENE=BMP5	GT:AD:DP:GQ:PL	0/1:176,162:338:99:5271,0,5457
-chr6	55848128	rs6911711	C	T	57.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.09;SOR=1.179;VQSLOD=8.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:85,9,0
-chr6	55924214	rs3830813	TC	T	169.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.073;ClippingRankSum=0.583;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.869;POSITIVE_TRAIN_SITE;QD=13.06;ReadPosRankSum=0.779;SOR=0.693;VQSLOD=6.26;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:6,6:12:99:207,0,206
-chr6	55926067	rs181810990	T	A	105.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.55;ClippingRankSum=0.55;DB;DP=7;FS=3.68;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.55;QD=15.11;ReadPosRankSum=-0.937;SOR=2.494;VQSLOD=1.41;culprit=ReadPosRankSum;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:3,4:7:92:134,0,92
-chr6	55929347	rs2235735	T	C	2151.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.816;ClippingRankSum=1.043;DB;DP=139;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.87;MQ0=0;MQRankSum=1.492;POSITIVE_TRAIN_SITE;QD=15.48;ReadPosRankSum=2.796;SOR=0.714;VQSLOD=2.9;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:63,75:138:99:2180,0,1872
-chr6	55929582	rs80177427	C	T	195.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.989;ClippingRankSum=0.0;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.264;POSITIVE_TRAIN_SITE;QD=10.88;ReadPosRankSum=-0.996;SOR=0.368;VQSLOD=4.38;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:11,7:18:99:224,0,344
-chr6	55932035	rs138548441	A	AT	3804.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.471;ClippingRankSum=-0.649;DB;DP=235;FS=5.07;MLEAC=1;MLEAF=0.5;MQ=60.13;MQ0=0;MQRankSum=-0.423;QD=16.19;ReadPosRankSum=-0.407;SOR=1.173;VQSLOD=-0.7158;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:134,100:234:99:3842,0,6908
-chr6	55932036	rs62406152	C	T	3813.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.075;ClippingRankSum=1.08;DB;DP=238;FS=5.079;MLEAC=1;MLEAF=0.5;MQ=60.22;MQ0=0;MQRankSum=1.382;QD=16.02;ReadPosRankSum=-0.395;SOR=1.179;VQSLOD=-0.069;culprit=DP;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:136,102:238:99:3842,0,6908
-chr6	55932278	rs12209529	C	T	994.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.948;ClippingRankSum=0.169;DB;DP=74;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.664;POSITIVE_TRAIN_SITE;QD=13.44;ReadPosRankSum=0.071;SOR=0.463;VQSLOD=4.42;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:42,32:74:99:1023,0,1552
-chr6	55932511	rs9396171	A	G	64.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.8;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	55933942	rs12189567	A	G	1295.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.173;ClippingRankSum=0.118;DB;DP=97;FS=4.397;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=13.36;ReadPosRankSum=-0.265;SOR=0.278;VQSLOD=2.33;culprit=DP;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:53,43:96:99:1324,0,1752
-chr6	55933987	rs12189571	A	C	812.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.663;ClippingRankSum=-0.455;DB;DP=59;FS=5.997;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.675;POSITIVE_TRAIN_SITE;QD=13.78;ReadPosRankSum=1.539;SOR=2.506;VQSLOD=2.27;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:33,25:58:99:841,0,1009
-chr6	55935196	rs17218309	G	A	45.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.2;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	55935617	rs41271338	T	C	3245.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.63;ClippingRankSum=-1.316;DB;DP=211;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.833;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=-0.759;SOR=0.734;VQSLOD=1.27;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:104,107:211:99:3274,0,3061
-chr6	55935791	rs1028390	T	C	301.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.261;ClippingRankSum=1.01;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.78;POSITIVE_TRAIN_SITE;QD=17.75;ReadPosRankSum=-0.241;SOR=0.804;VQSLOD=5.58;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:8,9:17:99:330,0,267
-chr6	55938839	rs4715576	G	A	104.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.774;ClippingRankSum=-0.099;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.296;POSITIVE_TRAIN_SITE;QD=5.82;ReadPosRankSum=-0.591;SOR=0.616;VQSLOD=4.82;culprit=QD;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:13,5:18:99:133,0,453
-chr6	55942538	rs969513	G	T	175.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=1.022;VQSLOD=6.0;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,5:5:15:204,15,0
-chr6	55942643	rs3065899	CAT	C	36.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.24;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.76;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:1,2:3:41:74,0,41
-chr6	55942956	rs17218770	C	G	1775.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.357;ClippingRankSum=0.32;DB;DP=106;FS=6.993;MLEAC=1;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=1.655;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=1.003;SOR=0.281;VQSLOD=1.69;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:50,56:106:99:1804,0,1640
-chr6	55943073	rs76049205	T	C	470.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.873;ClippingRankSum=1.669;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.003;POSITIVE_TRAIN_SITE;QD=21.4;ReadPosRankSum=1.135;SOR=1.085;VQSLOD=4.22;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:9,13:22:99:499,0,281
-chr6	55943101	rs62404861	C	A	242.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.366;ClippingRankSum=-0.34;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.34;POSITIVE_TRAIN_SITE;QD=16.18;ReadPosRankSum=1.324;SOR=0.818;VQSLOD=5.66;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:7,8:15:99:271,0,258
-chr6	55966027	rs12206920	C	G	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.91;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	55966418	rs4379279	A	G	640.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=5.67;VQSLOD=6.76;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,16:16:48:669,48,0
-chr6	55988619	rs41464152	T	C	84.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.19;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=6.5;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:1,3:4:28:113,0,28
-chr6	55988796	rs150586735	TTA	T	665.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.931;ClippingRankSum=-0.589;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.65;MQ0=0;MQRankSum=-1.804;POSITIVE_TRAIN_SITE;QD=20.8;ReadPosRankSum=0.285;SOR=0.957;VQSLOD=5.92;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:14,18:32:99:703,0,546
-chr6	55988837	.	CT	C	386.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.483;ClippingRankSum=-1.883;DP=57;FS=8.505;MLEAC=1;MLEAF=0.5;MQ=53.1;MQ0=0;MQRankSum=-0.083;POSITIVE_TRAIN_SITE;QD=6.78;ReadPosRankSum=0.276;SOR=2.91;VQSLOD=1.32;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:15,24:39:99:424,0,248
-chr6	55988932	rs41271844	T	C	1723.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.801;ClippingRankSum=0.515;DB;DP=108;FS=2.53;MLEAC=1;MLEAF=0.5;MQ=57.92;MQ0=0;MQRankSum=0.871;POSITIVE_TRAIN_SITE;QD=15.96;ReadPosRankSum=0.465;SOR=0.446;VQSLOD=2.59;culprit=DP;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:50,57:107:99:1752,0,1593
-chr6	55989320	rs12210901	T	C	81.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.537;ClippingRankSum=-0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=13.63;ReadPosRankSum=0.406;SOR=0.693;VQSLOD=6.07;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:3,3:6:97:110,0,97
-chr6	55990773	rs146607719	GTTTAC	G	82.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=-0.358;POSITIVE_TRAIN_SITE;QD=16.55;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=5.99;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:2,3:5:99:120,0,131
-chr6	56006672	rs10807510	C	T	2289.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=6.297;ClippingRankSum=-0.222;DB;DP=137;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.209;POSITIVE_TRAIN_SITE;QD=16.71;ReadPosRankSum=0.316;SOR=0.641;VQSLOD=3.89;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:67,70:137:99:2318,0,1931
-chr6	56021453	rs33997736	CTA	C	44.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.3;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	56021870	rs111577315	T	TAAA	789.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=29;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.38;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.23;SOR=5.892;VQSLOD=6.12;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,18:18:59:827,59,0
-chr6	56021985	rs1925180	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.13;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56021991	rs1925181	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.99;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56022644	rs9382583	C	T	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.9;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	56023811	rs994667	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56029832	rs10708181	AT	A	131.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=61.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.64;SOR=3.912;VQSLOD=6.42;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,6:6:18:169,18,0
-chr6	56031405	rs112307837	C	T	257.41	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.348;ClippingRankSum=0.696;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.393;POSITIVE_TRAIN_SITE;QD=23.4;ReadPosRankSum=0.696;SOR=3.258;VQSLOD=5.3;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:1,9:10:8:285,0,8
-chr6	56033094	rs35471617	G	A	1337.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.025;ClippingRankSum=-0.876;DB;DP=117;FS=1.69;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=1.143;POSITIVE_TRAIN_SITE;QD=11.43;ReadPosRankSum=1.054;SOR=0.91;VQSLOD=2.31;culprit=DP;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:70,47:117:99:1366,0,2112
-chr6	56037700	rs2397204	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56038131	rs9357892	A	C	266.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.16;SOR=1.609;VQSLOD=6.49;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,7:7:21:295,21,0
-chr6	56038152	rs1925186	C	G	388.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.093;VQSLOD=6.09;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,9:9:30:417,30,0
-chr6	56038178	rs9357893	G	A	104.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.447;ClippingRankSum=0.633;DB;DP=11;FS=6.99;MLEAC=1;MLEAF=0.5;MQ=56.09;MQ0=0;MQRankSum=1.447;POSITIVE_TRAIN_SITE;QD=9.52;ReadPosRankSum=0.365;SOR=3.258;VQSLOD=1.97;culprit=QD;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:6,4:10:99:133,0,206
-chr6	56038210	rs77593705	G	C	155.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.47;ClippingRankSum=-1.268;DB;DP=11;FS=5.441;MLEAC=1;MLEAF=0.5;MQ=58.29;MQ0=0;MQRankSum=0.336;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.47;SOR=0.662;VQSLOD=2.59;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	0/1:5,5:10:99:184,0,147
-chr6	56044578	rs2038149	T	C	10645.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=271;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.32;SOR=1.041;VQSLOD=2.44;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,271:271:99:10674,815,0
-chr6	56045043	rs2038150	C	A	1313.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=34;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=7.054;VQSLOD=6.76;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1342,99,0
-chr6	56045393	rs6933151	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56076639	rs6939465	A	C	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.31;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	56076688	rs6939632	C	T	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.35;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	56078396	rs6908195	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56080842	rs4126555	A	G	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	56090871	rs3846924	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56094789	rs1925147	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56135778	.	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56141614	rs141389271	G	GT	509.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.917;ClippingRankSum=0.694;DB;DP=108;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.93;MQ0=0;MQRankSum=0.858;QD=4.72;ReadPosRankSum=-0.709;SOR=0.467;VQSLOD=3.58;culprit=FS;GENE=DHFRP6,COL21A1	GT:AD:DP:GQ:PL	0/1:34,26:60:99:547,0,668
-chr6	56149855	rs9475651	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.83;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56149857	rs4715605	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.22;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56160179	rs4432980	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56163121	rs9396195	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56184256	rs4593354	T	C	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.25;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	56231275	rs60251615	GT	G	22.73	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=11.36;SOR=0.693;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:59,6,0
-chr6	56241523	rs6915564	T	G	134.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.51;SOR=3.258;VQSLOD=7.79;culprit=FS;GENE=COL21A1	GT:AD:DP:GQ:PL	1/1:0,4:4:12:162,12,0
-chr6	56271872	rs10456188	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56289250	rs623582	G	A	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	56357668	rs376190394	CA	C	95.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.642;ClippingRankSum=-0.049;DB;DP=93;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.6;MQ0=0;MQRankSum=1.135;QD=1.03;ReadPosRankSum=-0.148;SOR=0.156;VQSLOD=4.06;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:52,15:67:99:133,0,976
-chr6	56365814	rs4283892	A	G	5670.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=169;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.55;SOR=2.647;VQSLOD=4.88;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,169:169:99:5699,507,0
-chr6	56371698	rs9296848	A	G	6846.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=170;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.89;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.83;SOR=7.452;VQSLOD=5.12;culprit=QD;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,168:168:99:6875,506,0
-chr6	56373536	rs41271862	C	T	2810.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.287;ClippingRankSum=-0.385;DB;DP=179;FS=1.419;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.394;POSITIVE_TRAIN_SITE;QD=15.7;ReadPosRankSum=1.719;SOR=0.556;VQSLOD=2.22;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:86,93:179:99:2839,0,2900
-chr6	56374754	rs9296849	C	A	3283.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=86;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.38;SOR=6.689;VQSLOD=6.47;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3312,259,0
-chr6	56380064	rs5876514	CAT	C	739.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=18;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=62.94;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.2;SOR=5.892;VQSLOD=6.33;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,18:18:54:777,54,0
-chr6	56381912	rs4715626	G	A	9981.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.0;AN=2;BaseQRankSum=1.706;ClippingRankSum=-1.538;DB;DP=273;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;MQRankSum=-1.409;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.78;ReadPosRankSum=1.474;SOR=2.272;VQSLOD=-0.0057;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:1,267:268:99:10010,795,0
-chr6	56394173	rs9357922	T	C	2768.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=70;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.67;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=8.526;VQSLOD=7.41;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2797,210,0
-chr6	56395051	rs6939305	C	A	2021.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=52;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.27;SOR=7.941;VQSLOD=7.06;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2050,157,0
-chr6	56396694	rs34224935	CT	C	39.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.85;SOR=0.693;VQSLOD=7.81;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	56399731	rs7758054	A	T	964.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=25;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.5;SOR=6.518;VQSLOD=5.73;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,25:25:75:993,75,0
-chr6	56401999	rs4472350	G	A	91.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=9.11;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	56403072	.	G	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=DST	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	56410533	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56417282	rs4715630	C	T	12421.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=331;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.31;SOR=1.081;VQSLOD=3.29;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,331:331:99:12450,995,0
-chr6	56417545	rs4715631	T	C	10049.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=259;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.059;VQSLOD=4.04;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,259:259:99:10078,779,0
-chr6	56425284	rs2067543	A	G	1201.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.751;ClippingRankSum=0.059;DB;DP=57;FS=3.927;MLEAC=1;MLEAF=0.5;MQ=59.67;MQ0=0;MQRankSum=-0.652;POSITIVE_TRAIN_SITE;QD=21.08;ReadPosRankSum=0.296;SOR=0.22;VQSLOD=2.01;culprit=QD;GENE=DST	GT:AD:DP:GQ:PL	0/1:19,38:57:99:1230,0,587
-chr6	56425497	rs200368513	C	A	36.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.37;SOR=2.303;VQSLOD=6.64;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,2:2:6:64,6,0
-chr6	56425900	rs1884284	G	A	26.78	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=8.93;ReadPosRankSum=-0.736;SOR=1.179;GENE=DST	GT:AD:DP:GQ:PL	0/1:1,2:3:35:55,0,35
-chr6	56425921	rs1884285	T	A	80.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.92;ClippingRankSum=0.684;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=8.97;ReadPosRankSum=0.684;SOR=1.179;VQSLOD=4.63;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:4,5:9:99:118,0,116
-chr6	56425971	rs1884286	A	G	590.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.542;ClippingRankSum=-0.814;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.374;POSITIVE_TRAIN_SITE;QD=19.69;ReadPosRankSum=-0.33;SOR=1.536;VQSLOD=5.66;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:10,20:30:99:619,0,310
-chr6	56426562	rs9357923	G	A	403.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.202;ClippingRankSum=-0.527;DB;DP=23;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.837;POSITIVE_TRAIN_SITE;QD=17.56;ReadPosRankSum=-0.155;SOR=0.963;VQSLOD=5.73;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:10,13:23:99:432,0,331
-chr6	56426931	rs9367689	C	T	2689.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.37;ClippingRankSum=0.043;DB;DP=192;FS=4.778;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-0.486;POSITIVE_TRAIN_SITE;QD=14.01;ReadPosRankSum=2.114;SOR=0.409;VQSLOD=2.13;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:95,96:191:99:2718,0,3023
-chr6	56427095	rs79573569	C	CTGAGTGTTGAAA	1073.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.359;ClippingRankSum=0.523;DB;DP=57;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.02;MQ0=0;MQRankSum=-4.897;POSITIVE_TRAIN_SITE;QD=18.84;ReadPosRankSum=-1.568;SOR=0.483;VQSLOD=0.98;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:32,25:57:99:1111,0,1888
-chr6	56437465	rs1014309	T	C	1445.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.09;ClippingRankSum=0.209;DB;DP=89;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.79;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=16.24;ReadPosRankSum=1.427;SOR=0.648;VQSLOD=5.2;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:45,43:88:99:1474,0,1510
-chr6	56437902	rs2144405	C	T	1056.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.383;ClippingRankSum=0.809;DB;DP=66;FS=1.316;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.951;POSITIVE_TRAIN_SITE;QD=16.01;ReadPosRankSum=-1.516;SOR=0.461;VQSLOD=2.55;culprit=ReadPosRankSum;GENE=DST	GT:AD:DP:GQ:PL	0/1:31,35:66:99:1085,0,1085
-chr6	56453346	rs6919941	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56458332	.	T	A	301.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.437;ClippingRankSum=0.441;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.13;MQ0=0;MQRankSum=-3.737;QD=10.78;ReadPosRankSum=-1.927;SOR=0.46;VQSLOD=-0.8078;culprit=MQRankSum;GENE=DST	GT:AD:DP:GQ:PL	0/1:16,12:28:99:330,0,2663
-chr6	56458334	.	G	A	282.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.666;ClippingRankSum=0.476;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.14;MQ0=0;MQRankSum=-3.134;QD=8.84;ReadPosRankSum=-0.992;SOR=0.26;VQSLOD=0.189;culprit=MQRankSum;GENE=DST	GT:AD:DP:GQ:PL	0/1:21,11:32:99:311,0,3242
-chr6	56458337	.	G	A	260.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.343;ClippingRankSum=-0.083;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.95;MQ0=0;MQRankSum=-3.199;QD=6.86;ReadPosRankSum=-0.878;SOR=0.134;VQSLOD=-0.4171;culprit=MQRankSum;GENE=DST	GT:AD:DP:GQ:PL	0/1:28,10:38:99:289,0,3630
-chr6	56458338	.	T	A	215.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=4.133;ClippingRankSum=-0.659;DP=39;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.08;MQ0=0;MQRankSum=-3.522;NEGATIVE_TRAIN_SITE;QD=5.53;ReadPosRankSum=-2.3;SOR=0.126;VQSLOD=-2.429;culprit=MQRankSum;GENE=DST	GT:AD:DP:GQ:PL	0/1:29,10:39:99:244,0,3725
-chr6	56458339	.	AGGCT	A	206.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.653;ClippingRankSum=-1.136;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.56;MQ0=0;MQRankSum=-3.349;QD=4.81;ReadPosRankSum=-3.027;SOR=0.1;VQSLOD=-0.5999;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:33,10:43:99:244,0,3725
-chr6	56462840	rs9370541	G	A	2994.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.431;ClippingRankSum=-1.553;DB;DP=213;FS=6.435;MLEAC=1;MLEAF=0.5;MQ=59.78;MQ0=0;MQRankSum=0.686;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.54;SOR=1.216;VQSLOD=2.1;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:118,95:213:99:3023,0,3656
-chr6	56463410	rs4712138	T	C	5519.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.361;ClippingRankSum=-0.682;DB;DP=398;FS=13.317;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=0.637;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.87;ReadPosRankSum=2.315;SOR=0.352;VQSLOD=-0.4795;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:208,189:397:99:5548,0,6660
-chr6	56466999	rs9382653	T	G	75.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=6.62;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:2,3:5:63:104,0,63
-chr6	56467586	rs11751914	G	A	530.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.043;ClippingRankSum=1.304;DB;DP=35;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.403;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.601;SOR=0.641;VQSLOD=5.46;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:18,17:35:99:559,0,665
-chr6	56468238	rs9370543	G	A	3348.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=8.795;ClippingRankSum=0.055;DB;DP=200;FS=1.921;MLEAC=1;MLEAF=0.5;MQ=59.77;MQ0=0;MQRankSum=0.619;POSITIVE_TRAIN_SITE;QD=16.74;ReadPosRankSum=2.983;SOR=0.871;VQSLOD=2.18;culprit=ReadPosRankSum;GENE=DST	GT:AD:DP:GQ:PL	0/1:102,97:199:99:3377,0,3183
-chr6	56468537	rs9382656	T	C	5633.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=8.003;ClippingRankSum=-2.016;DB;DP=287;FS=2.022;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.379;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.63;ReadPosRankSum=-1.151;SOR=0.827;VQSLOD=0.525;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:124,162:286:99:5662,0,3728
-chr6	56470551	rs13194995	T	A	4264.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.507;ClippingRankSum=-0.154;DB;DP=311;FS=0.415;MLEAC=1;MLEAF=0.5;MQ=59.87;MQ0=0;MQRankSum=-0.365;POSITIVE_TRAIN_SITE;QD=13.71;ReadPosRankSum=0.256;SOR=0.662;VQSLOD=1.73;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:169,141:310:99:4293,0,5525
-chr6	56470690	rs13209548	G	A	4581.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.221;ClippingRankSum=0.043;DB;DP=298;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.85;MQ0=0;MQRankSum=-1.592;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=1.757;SOR=0.668;VQSLOD=1.27;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:151,147:298:99:4610,0,4504
-chr6	56471402	rs9382658	G	A	5089.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.363;ClippingRankSum=0.422;DB;DP=342;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.581;POSITIVE_TRAIN_SITE;QD=14.88;ReadPosRankSum=0.721;SOR=0.676;VQSLOD=1.79;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:182,158:340:99:5118,0,6087
-chr6	56471995	rs16888055	C	T	2905.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.315;ClippingRankSum=0.444;DB;DP=194;FS=5.194;MLEAC=1;MLEAF=0.5;MQ=59.69;MQ0=0;MQRankSum=0.379;POSITIVE_TRAIN_SITE;QD=14.98;ReadPosRankSum=1.462;SOR=1.052;VQSLOD=2.3;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:97,95:192:99:2934,0,3313
-chr6	56476023	rs9370544	G	A	43.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.14;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:1,2:3:27:72,0,27
-chr6	56476182	rs10643818	T	TAAGTA	257.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.783;ClippingRankSum=0.79;DB;DP=31;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.17;MQ0=0;MQRankSum=-1.828;POSITIVE_TRAIN_SITE;QD=8.31;ReadPosRankSum=-0.384;SOR=0.132;VQSLOD=5.82;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:23,8:31:99:295,0,1187
-chr6	56476262	rs7747060	T	C	1532.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.526;ClippingRankSum=-0.045;DB;DP=116;FS=1.204;MLEAC=1;MLEAF=0.5;MQ=58.89;MQ0=0;MQRankSum=-0.777;POSITIVE_TRAIN_SITE;QD=13.21;ReadPosRankSum=-0.453;SOR=0.898;VQSLOD=2.87;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:67,49:116:99:1561,0,2190
-chr6	56476456	rs9396226	T	A	997.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.112;ClippingRankSum=0.345;DB;DP=87;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.47;MQ0=0;MQRankSum=0.224;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.466;SOR=0.98;VQSLOD=4.8;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:34,44:78:99:1035,0,1041
-chr6	56482704	rs9396228	A	C	747.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.823;ClippingRankSum=-0.173;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.209;POSITIVE_TRAIN_SITE;QD=10.39;ReadPosRankSum=2.168;SOR=0.735;VQSLOD=4.91;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:48,24:72:99:776,0,1600
-chr6	56482801	rs6459166	C	G	2911.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.925;ClippingRankSum=0.679;DB;DP=217;FS=5.006;MLEAC=1;MLEAF=0.5;MQ=59.66;MQ0=0;MQRankSum=0.577;POSITIVE_TRAIN_SITE;QD=13.42;ReadPosRankSum=1.457;SOR=1.052;VQSLOD=2.17;culprit=DP;GENE=DST	GT:AD:DP:GQ:PL	0/1:119,98:217:99:2940,0,3555
-chr6	56484758	rs2230862	C	T	1769.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.905;ClippingRankSum=1.335;DB;DP=147;FS=6.412;MLEAC=1;MLEAF=0.5;MQ=56.34;MQ0=0;MQRankSum=1.822;POSITIVE_TRAIN_SITE;QD=12.04;ReadPosRankSum=0.721;SOR=0.357;VQSLOD=1.58;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:86,61:147:99:1798,0,2992
-chr6	56496649	rs10456737	A	C	1638.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.101;ClippingRankSum=-1.291;DB;DP=80;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.42;MQ0=0;MQRankSum=-0.16;POSITIVE_TRAIN_SITE;QD=20.48;ReadPosRankSum=0.671;SOR=0.763;VQSLOD=5.14;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1667,0,816
-chr6	56507135	rs1024195	T	C	1136.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.677;ClippingRankSum=0.952;DB;DP=56;FS=1.927;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=20.3;ReadPosRankSum=-0.108;SOR=1.511;VQSLOD=2.71;culprit=QD;GENE=DST	GT:AD:DP:GQ:PL	0/1:24,32:56:99:1165,0,749
-chr6	56701620	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.5;MQ0=0;QD=10.88;SOR=0.693;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56736574	.	TA	T	49.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.817;ClippingRankSum=1.184;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.89;MQ0=0;MQRankSum=0.531;QD=1.91;ReadPosRankSum=1.312;SOR=0.602;VQSLOD=4.48;culprit=FS;GENE=DST,RPL17P26	GT:AD:DP:GQ:PL	0/1:10,9:19:87:87,0,131
-chr6	56818706	rs986245	T	C	816.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=24;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.03;SOR=2.925;VQSLOD=6.74;culprit=FS;GENE=DST	GT:AD:DP:GQ:PL	1/1:0,24:24:72:845,72,0
-chr6	56827628	rs9349841	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=BEND6	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56846334	rs9396247	A	G	342.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=4.615;VQSLOD=6.28;culprit=FS;GENE=BEND6	GT:AD:DP:GQ:PL	1/1:0,9:9:27:371,27,0
-chr6	56873069	rs6925819	T	C	1050.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=30;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.45;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.57;SOR=3.912;VQSLOD=6.47;culprit=FS;GENE=BEND6	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1079,90,0
-chr6	56893978	rs58747062	TC	T	28.71	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.35;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:65,6,0
-chr6	56894940	rs34180205	CG	C	106	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.2;SOR=3.258;VQSLOD=5.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:143,12,0
-chr6	56900699	rs3996934	C	T	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	56917538	rs6926980	G	A	2244.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.357;ClippingRankSum=0.056;DB;DP=147;FS=7.253;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.138;POSITIVE_TRAIN_SITE;QD=15.27;ReadPosRankSum=2.288;SOR=0.714;VQSLOD=2.13;culprit=FS;GENE=KIAA1586	GT:AD:DP:GQ:PL	0/1:74,73:147:99:2273,0,2345
-chr6	56919443	rs61740375	A	G	752.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.392;ClippingRankSum=-0.128;DB;DP=52;FS=10.283;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.769;POSITIVE_TRAIN_SITE;QD=14.48;ReadPosRankSum=1.044;SOR=0.065;VQSLOD=1.36;culprit=FS;GENE=KIAA1586	GT:AD:DP:GQ:PL	0/1:27,25:52:99:781,0,941
-chr6	56963708	rs9367711	T	G	789.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.396;ClippingRankSum=-0.682;DB;DP=55;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.513;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.295;SOR=0.729;VQSLOD=5.51;culprit=FS;GENE=ZNF451	GT:AD:DP:GQ:PL	0/1:27,28:55:99:818,0,939
-chr6	56994594	rs7758913	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ZNF451	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56998023	rs3757296	A	G	2007.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.613;ClippingRankSum=-0.822;DB;DP=133;FS=2.401;MLEAC=1;MLEAF=0.5;MQ=59.72;MQ0=0;MQRankSum=-0.518;POSITIVE_TRAIN_SITE;QD=15.1;ReadPosRankSum=-1.605;SOR=0.503;VQSLOD=2.33;culprit=ReadPosRankSum;GENE=ZNF451	GT:AD:DP:GQ:PL	0/1:64,67:131:99:2036,0,2080
-chr6	57006391	rs2273919	C	T	310.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.573;ClippingRankSum=-0.38;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=1.356;POSITIVE_TRAIN_SITE;QD=19.42;ReadPosRankSum=2.007;SOR=1.244;VQSLOD=5.45;culprit=FS;GENE=ZNF451	GT:AD:DP:GQ:PL	0/1:6,10:16:99:339,0,197
-chr6	57006933	rs2273921	T	C	1686.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.719;ClippingRankSum=0.791;DB;DP=136;FS=8.16;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.554;POSITIVE_TRAIN_SITE;QD=12.4;ReadPosRankSum=0.949;SOR=1.463;VQSLOD=2.01;culprit=FS;GENE=ZNF451	GT:AD:DP:GQ:PL	0/1:76,60:136:99:1715,0,2402
-chr6	57012930	rs3734738	C	T	2118.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.567;ClippingRankSum=-0.086;DB;DP=161;FS=1.455;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.46;POSITIVE_TRAIN_SITE;QD=13.16;ReadPosRankSum=-1.077;SOR=0.558;VQSLOD=2.37;culprit=DP;GENE=ZNF451	GT:AD:DP:GQ:PL	0/1:87,74:161:99:2147,0,2812
-chr6	57048458	rs9885757	C	T	476.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.695;ClippingRankSum=-0.057;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.28;MQ0=0;MQRankSum=0.057;POSITIVE_TRAIN_SITE;QD=14.9;ReadPosRankSum=0.019;SOR=0.693;VQSLOD=5.92;culprit=FS;GENE=BAG2	GT:AD:DP:GQ:PL	0/1:16,16:32:99:505,0,556
-chr6	57055354	rs1040461	C	T	2987.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.147;ClippingRankSum=-2.243;DB;DP=178;FS=1.9;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.75;POSITIVE_TRAIN_SITE;QD=16.79;ReadPosRankSum=0.605;SOR=0.855;VQSLOD=2.11;culprit=DP;GENE=RAB23	GT:AD:DP:GQ:PL	0/1:81,97:178:99:3016,0,2448
-chr6	57059820	rs9357940	T	G	252.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.739;ClippingRankSum=0.627;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.739;POSITIVE_TRAIN_SITE;QD=18.05;ReadPosRankSum=0.715;SOR=0.976;VQSLOD=6.0;culprit=FS;GENE=RAB23	GT:AD:DP:GQ:PL	0/1:6,8:14:99:281,0,187
-chr6	57074911	rs9357941	G	A	404.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.359;ClippingRankSum=-0.103;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.462;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=-1.538;SOR=0.693;VQSLOD=5.41;culprit=FS;GENE=RAB23	GT:AD:DP:GQ:PL	0/1:13,13:26:99:433,0,497
-chr6	57097549	rs223304	T	C	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57106426	rs223289	T	G	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	57163494	rs7770252	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57182297	rs1019210	C	T	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=6.13;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	57183869	.	A	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	57188889	rs79594432	A	T	460.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.171;ClippingRankSum=0.415;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.756;POSITIVE_TRAIN_SITE;QD=17.07;ReadPosRankSum=-0.512;SOR=0.922;VQSLOD=5.2;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:12,15:27:99:489,0,381
-chr6	57191021	rs11381745	A	AG	1131.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=39;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=61.1;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.02;SOR=7.054;VQSLOD=6.03;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1169,99,0
-chr6	57209749	rs9475860	C	T	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.37;SOR=2.303;VQSLOD=6.73;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	57209802	rs1024706	T	C	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.21;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	57209865	rs5876534	GA	G	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=7.46;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57209889	rs1024705	G	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.52;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57213782	rs7772897	A	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57213785	rs7755104	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.88;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57226182	rs17705499	C	T	51.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=12.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.47;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,3:4:29:80,0,29
-chr6	57228571	rs12193422	G	A	48.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.15;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:29:77,0,29
-chr6	57228598	rs6911124	A	G	51.79	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;QD=12.95;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.09;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,3:4:23:80,0,23
-chr6	57228685	rs6911177	A	G	123.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.38;ClippingRankSum=-0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.72;QD=20.63;ReadPosRankSum=-0.72;SOR=0.693;VQSLOD=4.71;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,4:6:99:152,0,126
-chr6	57228704	rs6934266	T	G	46.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;QD=9.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=4.4;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:3,2:5:75:75,0,154
-chr6	57228809	rs6911507	A	C	50.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.92;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:32:79,0,32
-chr6	57231331	rs2079934	G	T	32.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.36;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:32:61,0,32
-chr6	57231352	rs2397239	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57231354	rs2397240	A	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57232345	rs12200857	G	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:28:40,0,28
-chr6	57232902	rs62417969	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57234078	rs9464454	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57243144	rs12201524	G	A	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=4.21;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,154
-chr6	57243154	rs12201527	G	A	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=4.91;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,154
-chr6	57244492	rs7759919	T	C	24.78	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.572;ClippingRankSum=-1.067;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.572;QD=3.1;ReadPosRankSum=-1.067;SOR=0.169;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:6,2:8:53:53,0,209
-chr6	57244509	rs5011405	T	G	34.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.589;ClippingRankSum=1.589;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=4.35;ReadPosRankSum=-0.572;SOR=0.169;VQSLOD=5.46;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:6,2:8:63:63,0,213
-chr6	57244672	rs5011404	G	A	2178.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.306;ClippingRankSum=2.205;DB;DP=136;FS=2.003;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=-0.847;POSITIVE_TRAIN_SITE;QD=16.02;ReadPosRankSum=0.446;SOR=1.017;VQSLOD=2.92;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:66,70:136:99:2207,0,2213
-chr6	57244780	rs5011403	G	A	3287.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.453;ClippingRankSum=0.408;DB;DP=235;FS=0.51;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=0.808;QD=13.99;ReadPosRankSum=0.963;SOR=0.634;VQSLOD=0.424;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:123,112:235:99:3316,0,3653
-chr6	57244830	rs5011402	T	A	2187.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.318;ClippingRankSum=1.365;DB;DP=134;FS=4.341;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=-1.29;QD=16.33;ReadPosRankSum=0.292;SOR=0.162;VQSLOD=0.141;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:64,70:134:99:2216,0,2120
-chr6	57244893	rs5011401	T	C	609.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.502;ClippingRankSum=-0.431;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-2.26;POSITIVE_TRAIN_SITE;QD=17.93;ReadPosRankSum=2.018;SOR=0.811;VQSLOD=4.32;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:16,18:34:99:638,0,509
-chr6	57244979	rs5011400	G	A	91.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.54;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,3:5:99:120,0,137
-chr6	57244982	rs5011399	C	T	91.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.34;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,3:5:99:120,0,137
-chr6	57246581	rs62415468	T	A	183.85	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.742;ClippingRankSum=-0.742;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=-0.742;QD=26.26;ReadPosRankSum=-0.742;SOR=2.584;VQSLOD=3.61;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,6:7:17:212,0,17
-chr6	57246614	rs62415469	T	C	379.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.371;ClippingRankSum=-2.285;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.718;QD=25.32;ReadPosRankSum=-1.371;SOR=1.911;VQSLOD=3.76;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:4,11:15:99:408,0,118
-chr6	57246638	rs6913328	C	T	668.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.214;ClippingRankSum=-1.226;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.603;QD=20.9;ReadPosRankSum=1.654;SOR=1.284;VQSLOD=3.38;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:12,20:32:99:697,0,376
-chr6	57246708	rs6913779	G	T	1443.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-8.155;ClippingRankSum=0.128;DB;DP=141;FS=4.59;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-1.089;QD=10.24;ReadPosRankSum=-0.829;SOR=0.067;VQSLOD=-0.7831;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:92,49:141:99:1472,0,3506
-chr6	57246773	rs113849959	T	TAGG	4992.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.588;ClippingRankSum=0.124;DB;DP=309;FS=5.829;MLEAC=1;MLEAF=0.5;MQ=57.08;MQ0=0;MQRankSum=-3.483;NEGATIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=1.26;SOR=1.145;VQSLOD=-2.405;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:174,127:301:99:5030,0,7083
-chr6	57246785	rs62415470	A	C	5492.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=8.898;ClippingRankSum=-0.346;DB;DP=349;FS=1.043;MLEAC=1;MLEAF=0.5;MQ=57.28;MQ0=0;MQRankSum=-1.73;QD=15.74;ReadPosRankSum=1.758;SOR=0.781;VQSLOD=-0.7042;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:201,148:349:99:5521,0,7683
-chr6	57246815	rs6936571	T	C	5593.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=6.746;ClippingRankSum=-1.594;DB;DP=416;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.57;MQ0=0;MQRankSum=-1.167;NEGATIVE_TRAIN_SITE;QD=13.45;ReadPosRankSum=-1.267;SOR=0.707;VQSLOD=-1.509;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:229,187:416:99:5622,0,7181
-chr6	57246878	rs61753604	T	C	1938.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.885;ClippingRankSum=1.162;DB;DP=444;FS=0.65;MLEAC=1;MLEAF=0.5;MQ=58.81;MQ0=0;MQRankSum=-1.757;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=4.37;ReadPosRankSum=0.012;SOR=0.802;VQSLOD=-1.92;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:350,94:444:99:1967,0,13279
-chr6	57246884	rs6913546	A	G	7065.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=3.408;ClippingRankSum=-0.389;DB;DP=440;FS=0.524;MLEAC=1;MLEAF=0.5;MQ=58.7;MQ0=0;MQRankSum=-2.305;NEGATIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-1.094;SOR=0.63;VQSLOD=-2.286;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:227,212:439:99:7094,0,7015
-chr6	57246969	rs4256440	G	A	4783.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.872;ClippingRankSum=0.62;DB;DP=347;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.69;MQ0=0;MQRankSum=-0.808;QD=13.79;ReadPosRankSum=-0.427;SOR=0.712;VQSLOD=-0.486;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:182,163:345:99:4812,0,6048
-chr6	57246982	rs4585567	G	T	4000.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.751;ClippingRankSum=0.33;DB;DP=315;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.77;MQ0=0;MQRankSum=-0.546;QD=12.7;ReadPosRankSum=-0.935;SOR=0.712;VQSLOD=-0.553;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:174,139:313:99:4029,0,5824
-chr6	57247022	rs4382263	C	T	3135.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.094;ClippingRankSum=-0.825;DB;DP=206;FS=9.797;MLEAC=1;MLEAF=0.5;MQ=59.1;MQ0=0;MQRankSum=0.277;QD=15.22;ReadPosRankSum=0.532;SOR=1.811;VQSLOD=-0.0767;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:108,98:206:99:3164,0,3645
-chr6	57247093	rs4499918	A	T	892.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.606;ClippingRankSum=0.186;DB;DP=63;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.52;MQ0=0;MQRankSum=0.131;QD=14.17;ReadPosRankSum=-0.517;SOR=0.551;VQSLOD=2.59;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:34,29:63:99:921,0,1186
-chr6	57247108	rs4507595	G	A	668.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.825;ClippingRankSum=0.298;DB;DP=53;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.24;MQ0=0;MQRankSum=-0.262;QD=12.62;ReadPosRankSum=0.406;SOR=0.416;VQSLOD=3.79;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:31,22:53:99:697,0,1110
-chr6	57247121	rs4310040	T	C	577.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.37;ClippingRankSum=-1.834;DB;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.82;MQ0=0;MQRankSum=-0.849;QD=13.44;ReadPosRankSum=-0.382;SOR=0.428;VQSLOD=3.58;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:25,18:43:99:606,0,856
-chr6	57259789	rs149275162	C	A	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.23;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57259808	rs117189504	A	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57259820	rs114240725	C	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57260463	rs9475913	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57262992	rs2894847	A	G	11.83	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=11.83;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:38,3,0
-chr6	57263008	rs72871660	G	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.01;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57284914	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57296209	rs78775831	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=9.3;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57296216	rs80242777	C	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=9.3;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57296249	rs72873542	C	G	16.63	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=8.31;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	57303056	rs62401712	T	C	40.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=13.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.28;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:29:69,0,29
-chr6	57303102	rs62401713	A	G	15.43	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=5.14;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:1:41,0,1
-chr6	57307716	rs60930046	T	C	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.63;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57307784	rs60600423	C	G	73.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=24.43;SOR=1.179;VQSLOD=5.3;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:101,9,0
-chr6	57309839	rs5003056	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57310132	rs73750278	C	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57310138	rs73750279	C	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57310284	rs9464491	A	G	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=5.91;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57310326	rs73750281	T	G	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.47;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57310334	rs73750282	T	C	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.59;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57315082	rs12204748	G	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.08;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57325633	rs4715697	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57326248	rs2145339	A	G	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=7.07;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	57326568	rs9464502	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57330320	rs9382742	T	C	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.34;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57336157	rs9476010	G	A	30.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.38;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.38;QD=5.13;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=3.01;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:4,2:6:59:59,0,154
-chr6	57336243	rs9476012	G	A	39.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=9.94;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=3.79;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:68:68,0,78
-chr6	57336279	rs9476013	C	G	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=4.91;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,78
-chr6	57336284	rs9476014	A	G	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=12.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.33;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,78
-chr6	57336340	rs1570072	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57342040	rs13219968	T	C	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.17;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	57345089	rs5024768	G	C	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.41;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57347208	.	T	TG	21.73	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.87;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0
-chr6	57347800	rs34877937	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.09;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57347818	rs35142105	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.18;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57348150	rs34523439	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.16;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57348155	rs35239416	A	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.42;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57348440	rs34411188	A	G	50.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=1.11;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:28:79,0,28
-chr6	57348501	rs35975405	T	C	71.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.34;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	57348518	rs71221642	A	G	71.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.4;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	57348534	rs34153534	G	A	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.69;SOR=1.179;VQSLOD=7.24;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57348538	rs34509185	T	G	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=35.33;SOR=1.179;VQSLOD=6.95;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57349040	rs9476023	T	C	93.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=7.46;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	57349257	rs9476024	C	T	16.63	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.63;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	57349280	rs12198778	A	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=7.09;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	57349405	rs9476025	A	G	17.61	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.61;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:44,3,0
-chr6	57349426	rs9476026	C	T	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.34;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57349572	rs6929331	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.11;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57349576	rs4715714	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.46;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57350134	rs9367752	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57353249	rs4715715	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57355968	rs35947597	T	A	102.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=7.02;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	57355975	.	C	A	102.28	PASS	AC=2;AF=1.0;AN=2;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=5.89;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	57355995	rs36115431	G	A	102.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=6.91;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	57356611	rs9476033	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57358196	rs36181256	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57358870	rs4991170	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57358888	rs5876577	T	TC	37.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.85;SOR=0.693;VQSLOD=7.35;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	57362013	rs62399733	T	C	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:31:40,0,31
-chr6	57362029	rs73752496	A	G	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.73;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:74:81,0,74
-chr6	57362030	rs72877164	C	T	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.56;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:74:81,0,74
-chr6	57362057	rs12526351	G	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:36:40,0,36
-chr6	57364996	rs73755520	C	T	32.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=3.31;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:61:61,0,76
-chr6	57365151	rs5025370	T	C	47.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=5.0;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:35:76,0,35
-chr6	57366534	rs4715718	G	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.68;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57366536	rs4715719	A	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.49;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57368219	rs62400883	G	A	36.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=12.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.12;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:30:65,0,30
-chr6	57369510	rs62400894	A	G	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.89;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57371913	rs59066164	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371916	rs75944038	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371926	rs10949092	A	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371931	rs74978393	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371939	rs10949093	G	A	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.87;SOR=0.693;VQSLOD=7.42;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	57371962	rs10949094	T	A	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=6.34;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	57372104	rs2024986	T	C	162.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.512;ClippingRankSum=0.514;DB;DP=25;FS=5.528;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.091;QD=6.51;ReadPosRankSum=0.212;SOR=0.033;VQSLOD=0.457;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:18,7:25:99:191,0,669
-chr6	57372116	rs9382768	T	C	752.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.259;ClippingRankSum=0.589;DB;DP=29;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.589;QD=25.96;ReadPosRankSum=-0.778;SOR=1.688;VQSLOD=2.67;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:9,20:29:99:781,0,276
-chr6	57372126	rs9396314	C	G	253.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.17;ClippingRankSum=-1.868;DB;DP=35;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.51;POSITIVE_TRAIN_SITE;QD=7.25;ReadPosRankSum=0.698;SOR=0.129;VQSLOD=4.41;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:26,9:35:99:282,0,1018
-chr6	57372199	rs9382769	T	C	3132.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=8.094;ClippingRankSum=0.441;DB;DP=131;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.12;MQ0=0;MQRankSum=-0.586;QD=23.91;ReadPosRankSum=-0.007;SOR=1.47;VQSLOD=1.39;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:46,85:131:99:3161,0,1398
-chr6	57372361	rs9382770	C	A	10336.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.385;ClippingRankSum=-0.913;DB;DP=437;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.82;MQ0=0;MQRankSum=1.326;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.567;SOR=0.72;VQSLOD=-2.151;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:149,287:436:99:10365,0,4146
-chr6	57372365	rs9396315	A	G	3727.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.398;ClippingRankSum=-0.329;DB;DP=443;FS=0.613;MLEAC=1;MLEAF=0.5;MQ=58.84;MQ0=0;MQRankSum=3.315;NEGATIVE_TRAIN_SITE;QD=8.41;ReadPosRankSum=0.164;SOR=0.61;VQSLOD=-3.453;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:298,144:442:99:3756,0,10951
-chr6	57372374	rs68090917	CT	C	3672.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.835;ClippingRankSum=0.028;DB;DP=420;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.5;MQ0=0;MQRankSum=0.217;POSITIVE_TRAIN_SITE;QD=8.74;ReadPosRankSum=0.275;SOR=0.674;VQSLOD=-0.1464;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:274,132:406:99:3710,0,8968
-chr6	57372436	rs9382771	G	C	4364.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=4.675;ClippingRankSum=0.15;DB;DP=201;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=-2.89;NEGATIVE_TRAIN_SITE;QD=21.72;ReadPosRankSum=0.305;SOR=1.373;VQSLOD=-1.61;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:74,127:201:99:4393,0,2326
-chr6	57372437	rs79221898	C	T	2323.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-9.294;ClippingRankSum=-0.543;DB;DP=202;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.44;MQ0=0;MQRankSum=0.03;QD=11.5;ReadPosRankSum=0.294;SOR=0.345;VQSLOD=0.165;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:123,79:202:99:2352,0,4259
-chr6	57372456	rs35141035	AT	A	952.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.481;ClippingRankSum=0.386;DB;DP=149;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.01;MQ0=0;MQRankSum=-1.225;POSITIVE_TRAIN_SITE;QD=6.39;ReadPosRankSum=0.325;SOR=0.544;VQSLOD=3.61;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:65,50:115:99:990,0,1228
-chr6	57372480	rs79601039	A	G	1090.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.462;ClippingRankSum=-0.042;DB;DP=82;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.03;MQ0=0;MQRankSum=0.276;QD=13.3;ReadPosRankSum=1.108;SOR=0.482;VQSLOD=3.82;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:46,36:82:99:1119,0,1889
-chr6	57372502	rs9349872	G	A	894.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.559;ClippingRankSum=-0.64;DB;DP=44;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.08;MQ0=0;MQRankSum=-3.815;QD=20.34;ReadPosRankSum=-0.166;SOR=0.99;VQSLOD=0.816;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:19,25:44:99:923,0,664
-chr6	57372510	rs77697887	T	G	453.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.557;ClippingRankSum=0.318;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-3.102;QD=11.94;ReadPosRankSum=-1.226;SOR=0.307;VQSLOD=0.504;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:24,14:38:99:482,0,966
-chr6	57372514	rs77868044	T	C	425.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.126;ClippingRankSum=0.397;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.03;MQ0=0;MQRankSum=-1.547;QD=13.31;ReadPosRankSum=-1.389;SOR=0.26;VQSLOD=2.8;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:21,11:32:99:454,0,927
-chr6	57372523	rs10706124	TG	T	235.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.127;ClippingRankSum=0.381;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.16;MQ0=0;MQRankSum=-3.433;POSITIVE_TRAIN_SITE;QD=8.42;ReadPosRankSum=1.704;SOR=0.169;VQSLOD=2.42;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:20,8:28:99:273,0,858
-chr6	57372526	rs10635932	C	CTTTA	238.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.25;ClippingRankSum=1.472;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.24;MQ0=0;MQRankSum=-3.139;POSITIVE_TRAIN_SITE;QD=9.18;ReadPosRankSum=1.694;SOR=0.202;VQSLOD=2.74;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:18,8:26:99:276,0,816
-chr6	57372583	rs9367754	C	T	93.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=-0.937;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.17;MQ0=0;MQRankSum=-0.937;QD=13.4;ReadPosRankSum=0.0;SOR=0.941;VQSLOD=4.53;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:3,4:7:99:122,0,108
-chr6	57372611	rs9382772	C	T	32.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=3.39;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:61:61,0,77
-chr6	57374364	rs75332238	C	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	57379671	rs4573085	C	G	43.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;QD=10.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=4.49;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,3:4:24:72,0,24
-chr6	57379715	rs2894901	T	G	98.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=24.51;SOR=1.609;VQSLOD=5.93;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,4:4:12:126,12,0
-chr6	57379745	rs9476056	G	A	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.66;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57384745	rs75634578	T	C	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.95;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57385801	rs4715735	A	G	39.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=19.87;SOR=0.693;VQSLOD=6.75;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-chr6	57386904	rs149764231	GAGA	G	43.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=2.5;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57389299	rs375498702	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57390094	rs12203268	T	C	12.06	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:25:40,0,25
-chr6	57390107	rs200901455	CATCTGTT	C	40.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=10.18;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=5.2;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,78
-chr6	57390124	rs56102916	G	C	111.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=27.76;SOR=0.693;VQSLOD=5.73;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,4:4:12:139,12,0
-chr6	57390134	rs75555855	C	T	26.78	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=6.69;ReadPosRankSum=1.026;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:55:55,0,78
-chr6	57390168	rs78919924	C	T	29.78	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.804;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:27:58,0,27
-chr6	57392874	rs927195	C	T	110.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.72;QD=18.46;ReadPosRankSum=0.0;SOR=0.368;VQSLOD=4.73;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,4:6:61:139,0,61
-chr6	57392913	rs927194	T	C	103.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;ClippingRankSum=-1.638;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.05;MQ0=0;MQRankSum=1.368;POSITIVE_TRAIN_SITE;QD=12.97;ReadPosRankSum=-0.922;SOR=0.693;VQSLOD=6.21;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:4,4:8:99:132,0,222
-chr6	57392921	rs62398963	T	A	88.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.312;ClippingRankSum=-1.157;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.2;MQ0=0;MQRankSum=-0.231;QD=6.83;ReadPosRankSum=-0.386;SOR=0.223;VQSLOD=3.71;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:9,4:13:99:117,0,346
-chr6	57392963	rs927193	T	C	531.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.951;ClippingRankSum=-0.11;DB;DP=29;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.39;MQ0=0;MQRankSum=0.68;QD=18.34;ReadPosRankSum=-0.811;SOR=0.906;VQSLOD=3.89;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:13,16:29:99:560,0,435
-chr6	57393029	rs77090024	T	A	813.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=3.045;ClippingRankSum=0.061;DB;DP=76;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-4.889;NEGATIVE_TRAIN_SITE;QD=10.71;ReadPosRankSum=2.576;SOR=0.201;VQSLOD=-3.073;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:52,24:76:99:842,0,2229
-chr6	57393034	rs75127850	G	T	1008.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.248;ClippingRankSum=0.023;DB;DP=86;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.5;MQ0=0;MQRankSum=-5.58;NEGATIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=1.286;SOR=0.216;VQSLOD=-3.258;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:58,28:86:99:1037,0,2424
-chr6	57393040	rs74756458	A	T	1158.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.499;ClippingRankSum=-1.753;DB;DP=96;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.21;MQ0=0;MQRankSum=-5.165;NEGATIVE_TRAIN_SITE;QD=12.07;ReadPosRankSum=1.667;SOR=0.229;VQSLOD=-3.001;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:64,32:96:99:1187,0,2672
-chr6	57393054	rs75725892	G	A	1341.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=8.421;ClippingRankSum=0.555;DB;DP=120;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.42;MQ0=0;MQRankSum=-4.298;NEGATIVE_TRAIN_SITE;QD=11.18;ReadPosRankSum=1.283;SOR=1.179;VQSLOD=-2.209;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:81,39:120:99:1370,0,3620
-chr6	57393074	rs73752376	A	G	1772.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=7.296;ClippingRankSum=0.236;DB;DP=171;FS=3.973;MLEAC=1;MLEAF=0.5;MQ=56.54;MQ0=0;MQRankSum=-2.664;NEGATIVE_TRAIN_SITE;QD=10.37;ReadPosRankSum=0.65;SOR=1.329;VQSLOD=-1.602;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:121,50:171:99:1801,0,5032
-chr6	57393092	rs73752377	T	A	2197.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=2.298;ClippingRankSum=0.412;DB;DP=234;FS=2.43;MLEAC=1;MLEAF=0.5;MQ=56.7;MQ0=0;MQRankSum=-2.781;NEGATIVE_TRAIN_SITE;QD=9.39;ReadPosRankSum=-0.722;SOR=0.915;VQSLOD=-1.964;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:164,70:234:99:2226,0,6218
-chr6	57393125	rs927192	A	G	7635.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=5.292;ClippingRankSum=-0.772;DB;DP=356;FS=5.93;MLEAC=1;MLEAF=0.5;MQ=57.99;MQ0=0;MQRankSum=0.055;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.45;ReadPosRankSum=-0.84;SOR=0.43;VQSLOD=-0.2175;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:129,227:356:99:7664,0,3693
-chr6	57393160	rs76686926	G	A	2805.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.132;ClippingRankSum=0.139;DB;DP=395;FS=1.817;MLEAC=1;MLEAF=0.5;MQ=57.77;MQ0=0;MQRankSum=-1.496;NEGATIVE_TRAIN_SITE;QD=7.1;ReadPosRankSum=0.029;SOR=0.592;VQSLOD=-2.787;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:278,117:395:99:2834,0,8784
-chr6	57393199	rs2397502	C	A	3769.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.119;ClippingRankSum=1.716;DB;DP=344;FS=1.419;MLEAC=1;MLEAF=0.5;MQ=58.31;MQ0=0;MQRankSum=2.244;NEGATIVE_TRAIN_SITE;QD=10.96;ReadPosRankSum=0.093;SOR=0.606;VQSLOD=-1.342;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:226,118:344:99:3798,0,8416
-chr6	57393216	rs2397503	G	T	6455.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-7.047;ClippingRankSum=0.677;DB;DP=273;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.46;MQ0=0;MQRankSum=-1.274;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.802;SOR=0.672;VQSLOD=-1.677;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:112,161:273:99:6484,0,4010
-chr6	57393222	rs111989160	A	G	2124.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=6.075;ClippingRankSum=0.447;DB;DP=254;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.63;MQ0=0;MQRankSum=-0.081;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=1.798;SOR=0.705;VQSLOD=-1.47;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:191,63:254:99:2153,0,7932
-chr6	57393228	rs112156516	G	A	2056.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=7.272;ClippingRankSum=-0.141;DB;DP=242;FS=2.168;MLEAC=1;MLEAF=0.5;MQ=58.56;MQ0=0;MQRankSum=0.518;NEGATIVE_TRAIN_SITE;QD=8.5;ReadPosRankSum=2.889;SOR=1.002;VQSLOD=-1.477;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:182,60:242:99:2085,0,7456
-chr6	57393278	rs75909609	T	C	978.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=7.163;ClippingRankSum=1.948;DB;DP=126;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.86;MQ0=0;MQRankSum=0.294;QD=7.77;ReadPosRankSum=0.566;SOR=0.428;VQSLOD=1.81;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:93,33:126:99:1007,0,3194
-chr6	57393323	rs12198995	T	C	122.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.995;ClippingRankSum=-0.894;DB;DP=63;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.03;MQ0=0;MQRankSum=-1.012;QD=1.95;ReadPosRankSum=0.953;SOR=0.033;VQSLOD=0.768;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:54,9:63:99:151,0,2049
-chr6	57393329	rs76564922	G	T	491.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.488;ClippingRankSum=-0.148;DB;DP=58;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.67;MQ0=0;MQRankSum=1.018;QD=8.48;ReadPosRankSum=0.478;SOR=0.145;VQSLOD=3.43;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:42,16:58:99:520,0,1666
-chr6	57393337	rs200714656	T	TA	779.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.011;ClippingRankSum=0.247;DB;DP=47;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.61;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=16.59;ReadPosRankSum=-0.957;SOR=0.446;VQSLOD=5.5;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:27,20:47:99:817,0,1052
-chr6	57393338	rs2397504	T	A	1418.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.401;ClippingRankSum=0.911;DB;DP=45;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.36;MQ0=0;MQRankSum=-1.809;NEGATIVE_TRAIN_SITE;QD=31.53;ReadPosRankSum=-1.578;SOR=2.059;VQSLOD=-0.2208;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:12,33:45:99:1447,0,396
-chr6	57393350	rs2397505	G	A	577.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.397;ClippingRankSum=-0.51;DB;DP=37;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.72;MQ0=0;MQRankSum=-2.8;QD=15.62;ReadPosRankSum=-1.686;SOR=0.395;VQSLOD=1.1;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:22,15:37:99:606,0,861
-chr6	57393407	rs374979361	C	T	67.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.683;ClippingRankSum=-0.573;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.248;QD=7.53;ReadPosRankSum=-0.248;SOR=0.283;VQSLOD=4.48;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:6,3:9:96:96,0,194
-chr6	57393519	rs62398965	A	G	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.5;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57393716	rs2397508	G	A	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	57394939	rs11963080	C	T	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.21;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57395058	rs12202626	T	C	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.08;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57395077	rs12195527	C	G	61.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.87;SOR=2.303;VQSLOD=7.52;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:89,6,0
-chr6	57395396	rs74519885	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57396165	rs6924765	G	A	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.82;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:78:81,0,78
-chr6	57396173	rs79246915	G	T	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=4.76;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:78:81,0,78
-chr6	57397866	rs57276498	T	TA	68.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=0.0;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.82;MQ0=0;MQRankSum=-0.72;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.72;SOR=1.329;VQSLOD=5.96;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,4:6:38:106,0,38
-chr6	57397944	rs7770986	A	G	201.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.659;ClippingRankSum=-0.183;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.28;MQ0=0;MQRankSum=0.183;QD=5.93;ReadPosRankSum=-0.386;SOR=0.392;VQSLOD=2.5;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:26,8:34:99:230,0,866
-chr6	57397982	rs7771127	C	A	876.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.945;ClippingRankSum=-0.215;DB;DP=57;FS=3.087;MLEAC=1;MLEAF=0.5;MQ=56.94;MQ0=0;MQRankSum=-1.269;QD=15.38;ReadPosRankSum=0.567;SOR=0.197;VQSLOD=1.24;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:29,28:57:99:905,0,992
-chr6	57398008	rs7771257	C	T	1863.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.114;ClippingRankSum=-0.432;DB;DP=91;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=-1.126;QD=20.48;ReadPosRankSum=-0.093;SOR=0.232;VQSLOD=3.03;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:44,46:90:99:1892,0,1700
-chr6	57398009	rs7771114	A	G	1863.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.944;ClippingRankSum=0.703;DB;DP=92;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.26;MQ0=0;MQRankSum=-3.03;POSITIVE_TRAIN_SITE;QD=20.26;ReadPosRankSum=-0.203;SOR=0.241;VQSLOD=3.1;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:44,47:91:99:1892,0,1700
-chr6	57398028	rs67286646	TG	T	832.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.812;ClippingRankSum=-0.912;DB;DP=148;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.11;MQ0=0;MQRankSum=0.437;POSITIVE_TRAIN_SITE;QD=5.63;ReadPosRankSum=-0.426;SOR=0.853;VQSLOD=3.92;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:107,40:147:99:870,0,4153
-chr6	57398047	rs76081480	A	C	1782.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=7.353;ClippingRankSum=-0.762;DB;DP=191;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.74;MQ0=0;MQRankSum=-2.177;NEGATIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.084;SOR=0.701;VQSLOD=-1.736;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:127,63:190:99:1811,0,4583
-chr6	57398058	rs7771283	C	G	1588.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.421;ClippingRankSum=0.238;DB;DP=230;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.8;MQ0=0;MQRankSum=1.141;NEGATIVE_TRAIN_SITE;QD=6.91;ReadPosRankSum=-1.687;SOR=0.435;VQSLOD=-2.531;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:168,61:229:99:1617,0,5971
-chr6	57398081	rs7753294	T	G	5599.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=8.745;ClippingRankSum=0.077;DB;DP=263;FS=27.103;MLEAC=1;MLEAF=0.5;MQ=54.71;MQ0=0;MQRankSum=-4.145;NEGATIVE_TRAIN_SITE;QD=21.29;ReadPosRankSum=2.243;SOR=3.663;VQSLOD=-1.976;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:103,159:262:99:5628,0,3075
-chr6	57398117	rs139574925	T	TA	2948.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.101;ClippingRankSum=1.493;DB;DP=361;FS=2.214;MLEAC=1;MLEAF=0.5;MQ=54.59;MQ0=0;MQRankSum=-1.42;NEGATIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=-1.614;SOR=0.901;VQSLOD=-2.236;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:262,99:361:99:2986,0,10807
-chr6	57398118	rs147643173	G	T	2951.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-8.611;ClippingRankSum=0.472;DB;DP=366;FS=1.357;MLEAC=1;MLEAF=0.5;MQ=54.39;MQ0=0;MQRankSum=-1.61;NEGATIVE_TRAIN_SITE;QD=8.06;ReadPosRankSum=-1.741;SOR=0.841;VQSLOD=-2.741;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:265,101:366:99:2980,0,10921
-chr6	57398154	rs80081867	T	C	9900.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.712;ClippingRankSum=-1.351;DB;DP=417;FS=3.795;MLEAC=1;MLEAF=0.5;MQ=52.44;MQ0=0;MQRankSum=-5.322;NEGATIVE_TRAIN_SITE;QD=23.74;ReadPosRankSum=0.785;SOR=1.039;VQSLOD=-2.613;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:170,247:417:99:9929,0,6569
-chr6	57398157	rs9476080	A	G	10031.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=11.939;ClippingRankSum=-0.67;DB;DP=420;FS=5.63;MLEAC=1;MLEAF=0.5;MQ=52.56;MQ0=0;MQRankSum=-6.161;NEGATIVE_TRAIN_SITE;QD=23.89;ReadPosRankSum=1.335;SOR=1.089;VQSLOD=-2.877;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:174,246:420:99:10060,0,6871
-chr6	57398163	rs9476081	A	G	9691.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.386;ClippingRankSum=-0.317;DB;DP=428;FS=7.782;MLEAC=1;MLEAF=0.5;MQ=52.95;MQ0=0;MQRankSum=-7.057;NEGATIVE_TRAIN_SITE;QD=22.64;ReadPosRankSum=2.15;SOR=1.207;VQSLOD=-3.25;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:182,246:428:99:9720,0,6877
-chr6	57398186	rs147954160	G	GA	3146.73	VQSRTrancheINDEL99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=1.394;ClippingRankSum=0.081;DB;DP=466;FS=0.612;MLEAC=1;MLEAF=0.5;MQ=53.38;MQ0=0;MQRankSum=-5.529;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=6.75;ReadPosRankSum=-0.584;SOR=0.648;VQSLOD=-3.838;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:331,119:450:99:3184,0,13464
-chr6	57398201	rs62398997	T	C	9311.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=1.718;ClippingRankSum=0.323;DB;DP=477;FS=1.13;MLEAC=1;MLEAF=0.5;MQ=53.38;MQ0=0;MQRankSum=-2.722;NEGATIVE_TRAIN_SITE;QD=19.52;ReadPosRankSum=0.869;SOR=0.576;VQSLOD=-2.548;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:235,242:477:99:9340,0,8506
-chr6	57398207	rs71214816	G	T	3201.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.739;ClippingRankSum=0.609;DB;DP=476;FS=3.961;MLEAC=1;MLEAF=0.5;MQ=53.59;MQ0=0;MQRankSum=-5.623;NEGATIVE_TRAIN_SITE;QD=6.73;ReadPosRankSum=0.211;SOR=0.475;VQSLOD=-3.396;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:358,113:471:99:3230,0,14267
-chr6	57398226	rs77436138	T	G	5638.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=6.88;ClippingRankSum=1.585;DB;DP=474;FS=4.176;MLEAC=1;MLEAF=0.5;MQ=55.11;MQ0=0;MQRankSum=-0.678;NEGATIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=-1.594;SOR=0.924;VQSLOD=-2.787;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:202,185:387:99:5667,0,7682
-chr6	57398264	rs62398998	A	G	10505.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=7.8;ClippingRankSum=0.363;DB;DP=483;FS=5.181;MLEAC=1;MLEAF=0.5;MQ=56.66;MQ0=0;MQRankSum=-3.599;NEGATIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.128;SOR=0.919;VQSLOD=-2.719;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:185,297:482:99:10534,0,5426
-chr6	57398270	rs62398999	C	T	3777.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-8.082;ClippingRankSum=1.817;DB;DP=482;FS=4.566;MLEAC=1;MLEAF=0.5;MQ=56.75;MQ0=0;MQRankSum=-2.615;NEGATIVE_TRAIN_SITE;QD=7.84;ReadPosRankSum=0.627;SOR=1.059;VQSLOD=-3.182;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:338,143:481:99:3806,0,12584
-chr6	57398335	rs4715745	A	T	7297.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=0.878;ClippingRankSum=-0.623;DB;DP=391;FS=18.28;MLEAC=1;MLEAF=0.5;MQ=56.94;MQ0=0;MQRankSum=-1.096;NEGATIVE_TRAIN_SITE;QD=18.66;ReadPosRankSum=0.479;SOR=1.573;VQSLOD=-1.998;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:151,240:391:99:7326,0,4341
-chr6	57398385	rs11455120	A	AT	2033.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.004;ClippingRankSum=-0.159;DB;DP=270;FS=2.505;MLEAC=1;MLEAF=0.5;MQ=57.95;MQ0=0;MQRankSum=1.708;POSITIVE_TRAIN_SITE;QD=7.53;ReadPosRankSum=2.608;SOR=1.265;VQSLOD=-0.3154;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:165,71:236:99:2071,0,7214
-chr6	57398395	rs78658694	A	T	1426.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=5.633;ClippingRankSum=-0.557;DB;DP=246;FS=2.513;MLEAC=1;MLEAF=0.5;MQ=58.16;MQ0=0;MQRankSum=-1.385;NEGATIVE_TRAIN_SITE;QD=5.8;ReadPosRankSum=2.107;SOR=1.287;VQSLOD=-2.484;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:170,67:237:99:1455,0,7359
-chr6	57398412	rs6937166	A	G	1614.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=5.113;ClippingRankSum=0.84;DB;DP=201;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.23;MQ0=0;MQRankSum=0.045;NEGATIVE_TRAIN_SITE;QD=8.03;ReadPosRankSum=-0.11;SOR=0.142;VQSLOD=-1.257;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:145,56:201:99:1643,0,5481
-chr6	57398491	rs6937368	C	T	90.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.276;ClippingRankSum=0.17;DB;DP=40;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.42;MQ0=0;MQRankSum=-0.019;QD=2.27;ReadPosRankSum=-0.511;SOR=0.039;VQSLOD=1.26;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:34,6:40:99:119,0,1359
-chr6	57398503	rs4388290	A	G	387.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.279;ClippingRankSum=-0.151;DB;DP=36;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.36;MQ0=0;MQRankSum=-0.319;QD=10.77;ReadPosRankSum=-0.319;SOR=0.239;VQSLOD=2.63;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:24,12:36:99:416,0,1055
-chr6	57398517	rs4400219	C	A	314.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.503;ClippingRankSum=0.37;DB;DP=31;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.25;MQ0=0;MQRankSum=-0.196;QD=10.15;ReadPosRankSum=0.849;SOR=0.173;VQSLOD=3.45;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:22,9:31:99:343,0,999
-chr6	57398587	rs4506046	A	G	226.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.635;ClippingRankSum=-0.831;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.977;QD=18.9;ReadPosRankSum=1.977;SOR=1.022;VQSLOD=3.22;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:5,7:12:99:255,0,157
-chr6	57398921	.	T	C	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:36:40,0,36
-chr6	57398943	rs12203062	C	T	29.77	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=7.44;ReadPosRankSum=-1.026;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:58:58,0,78
-chr6	57404528	rs12528027	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57404529	rs71221626	G	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.19;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57404548	rs6934525	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57404559	rs6911998	G	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409216	rs487488	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409238	rs7757807	T	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409250	rs28431347	T	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409360	rs7775846	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57414331	rs522176	A	G	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.28;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57414352	rs522107	G	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57414355	rs577952	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57419091	rs11362490	AG	A	32.71	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=16.35;SOR=2.303;VQSLOD=8.34;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	57419145	rs482977	T	C	101.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.26;SOR=0.693;VQSLOD=7.58;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,4:4:12:129,12,0
-chr6	57419169	rs482916	C	T	96.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.09;SOR=1.179;VQSLOD=6.81;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	57419203	rs28444227	T	A	84.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.09;SOR=1.179;VQSLOD=6.21;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	57419529	rs5011343	C	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57419548	rs5011342	G	A	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.24;SOR=1.609;VQSLOD=4.67;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:6:70,6,0
-chr6	57419564	rs5011341	G	A	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.6;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57419593	rs5000703	G	T	60.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=6.82;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	57419621	rs5000702	C	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.18;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	57420055	rs973971	A	T	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=7.29;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	57420085	rs10678736	T	TGCAATA	43.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.61;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57420331	rs536921	A	G	45.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=11.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.6;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:33:74,0,33
-chr6	57420394	rs3903673	C	G	39.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.358;QD=7.95;ReadPosRankSum=1.231;SOR=1.609;VQSLOD=2.43;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:3,2:5:68:68,0,116
-chr6	57429628	rs9476125	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.39;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57429632	rs13200513	C	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57429655	rs13200414	A	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57429863	rs12194179	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57430291	rs12209094	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57430302	rs12195853	G	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.78;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57430787	rs9382792	A	G	66.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=5.69;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	57430868	rs9396334	C	T	14.68	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.68;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	57431267	rs2397534	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57436741	rs6924004	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57437720	rs519735	A	G	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=6.98;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	57437853	rs13212334	A	G	12.06	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:25:40,0,25
-chr6	57438133	rs1174361	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57438139	rs1174362	C	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57438156	rs78245671	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.19;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57440169	rs581096	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57440174	rs581102	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57440196	rs581193	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.05;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57440211	rs581228	T	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.37;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442438	rs5005193	C	G	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.36;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	57442463	rs5005192	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.31;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442488	rs4715782	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.25;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442506	rs5005191	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.49;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442507	rs5005190	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.99;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57443228	rs6913239	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57443255	rs1855414	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57447972	rs4715787	T	G	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=6.49;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	57454558	rs9357983	C	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57454567	rs62399084	A	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57454589	rs9357984	A	G	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.54;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57454920	rs9357986	C	T	55.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=18.43;SOR=1.179;VQSLOD=5.05;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:83,9,0
-chr6	57455443	rs7766809	A	G	98.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.76;SOR=1.179;VQSLOD=6.98;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:126,9,0
-chr6	57456136	rs4596481	T	C	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.86;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	57456931	rs79510351	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57456963	rs75987787	T	C	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.05;SOR=1.179;VQSLOD=6.12;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57456968	rs78473260	G	A	107.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.4;SOR=1.179;VQSLOD=6.89;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57457564	rs3805802	A	G	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.6;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57461356	rs62399146	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57463643	rs6905367	A	G	45.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.87;SOR=2.303;VQSLOD=7.58;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	57466787	rs6924157	G	C	81.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=-1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;QD=16.35;ReadPosRankSum=0.358;SOR=0.223;VQSLOD=5.23;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,3:5:59:110,0,59
-chr6	57466812	rs78692044	T	A	28.77	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=-0.72;QD=4.8;ReadPosRankSum=-0.72;SOR=1.179;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:4,2:6:57:57,0,146
-chr6	57466836	rs11411187	A	AC	203.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.067;ClippingRankSum=1.589;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.05;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=25.47;ReadPosRankSum=-1.067;SOR=0.693;VQSLOD=5.99;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,6:8:57:241,0,57
-chr6	57466844	rs12197381	G	A	64.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.573;ClippingRankSum=-0.573;DB;DP=9;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=57.39;MQ0=0;MQRankSum=0.248;QD=7.2;ReadPosRankSum=0.248;SOR=0.045;VQSLOD=0.706;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:6,3:9:93:93,0,212
-chr6	57466871	rs79082382	G	A	111.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.793;ClippingRankSum=0.244;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-2.141;QD=9.31;ReadPosRankSum=-0.529;SOR=0.446;VQSLOD=2.61;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:7,5:12:99:140,0,269
-chr6	57466891	rs12210717	A	T	431.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.484;ClippingRankSum=-0.698;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.45;MQ0=0;MQRankSum=-0.611;QD=20.56;ReadPosRankSum=0.349;SOR=0.941;VQSLOD=3.93;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:5,15:20:99:460,0,165
-chr6	57466915	rs12205876	T	A	732.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.992;ClippingRankSum=1.449;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=0.839;QD=26.17;ReadPosRankSum=1.297;SOR=0.402;VQSLOD=2.6;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:8,20:28:99:761,0,252
-chr6	57466922	rs2894917	T	C	1572.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=36;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.29;SOR=4.921;VQSLOD=6.55;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1601,111,0
-chr6	57466957	rs9885746	C	T	515.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.903;ClippingRankSum=-0.774;DB;DP=69;FS=3.021;MLEAC=1;MLEAF=0.5;MQ=57.62;MQ0=0;MQRankSum=-0.787;QD=7.47;ReadPosRankSum=-0.192;SOR=0.154;VQSLOD=-0.3023;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:49,20:69:99:544,0,2169
-chr6	57466958	rs12212128	A	G	1712.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.269;ClippingRankSum=0.064;DB;DP=74;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.81;MQ0=0;MQRankSum=-1.391;QD=23.15;ReadPosRankSum=-0.906;SOR=0.355;VQSLOD=2.47;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:24,50:74:99:1741,0,776
-chr6	57466969	rs12212129	A	G	1088.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=6.62;ClippingRankSum=-0.34;DB;DP=83;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.03;MQ0=0;MQRankSum=-0.237;QD=13.12;ReadPosRankSum=-0.386;SOR=0.362;VQSLOD=3.55;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:50,33:83:99:1117,0,1689
-chr6	57466987	rs12205887	T	C	1230.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.854;ClippingRankSum=-0.004;DB;DP=98;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=0.575;QD=12.56;ReadPosRankSum=-0.126;SOR=0.389;VQSLOD=3.29;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:58,40:98:99:1259,0,2007
-chr6	57467084	rs9885913	A	G	2211.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=4.628;ClippingRankSum=0.293;DB;DP=304;FS=4.869;MLEAC=1;MLEAF=0.5;MQ=58.78;MQ0=0;MQRankSum=-0.944;NEGATIVE_TRAIN_SITE;QD=7.28;ReadPosRankSum=3.057;SOR=1.014;VQSLOD=-2.572;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:233,71:304:99:2240,0,9850
-chr6	57467093	rs9885916	A	G	2301.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=7.069;ClippingRankSum=0.184;DB;DP=312;FS=3.079;MLEAC=1;MLEAF=0.5;MQ=58.58;MQ0=0;MQRankSum=-1.638;NEGATIVE_TRAIN_SITE;QD=7.38;ReadPosRankSum=0.912;SOR=0.918;VQSLOD=-2.342;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:239,73:312:99:2330,0,10451
-chr6	57467100	rs4535533	G	C	6947.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.106;ClippingRankSum=-2.135;DB;DP=314;FS=1.422;MLEAC=1;MLEAF=0.5;MQ=58.67;MQ0=0;MQRankSum=-0.67;NEGATIVE_TRAIN_SITE;QD=22.13;ReadPosRankSum=0.52;SOR=0.8;VQSLOD=-1.704;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:122,192:314:99:6976,0,3683
-chr6	57467107	rs9885751	C	T	1881.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=6.859;ClippingRankSum=-1.729;DB;DP=314;FS=5.484;MLEAC=1;MLEAF=0.5;MQ=58.52;MQ0=0;MQRankSum=-1.808;NEGATIVE_TRAIN_SITE;QD=5.99;ReadPosRankSum=0.287;SOR=1.037;VQSLOD=-2.38;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:238,76:314:99:1910,0,9279
-chr6	57467175	rs4406234	A	G	2889.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.932;ClippingRankSum=-0.383;DB;DP=258;FS=0.469;MLEAC=1;MLEAF=0.5;MQ=58.12;MQ0=0;MQRankSum=0.153;NEGATIVE_TRAIN_SITE;QD=11.2;ReadPosRankSum=4.087;SOR=0.741;VQSLOD=-0.735;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:159,99:258:99:2918,0,5132
-chr6	57467279	rs6459263	T	C	1140.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=5.633;ClippingRankSum=1.776;DB;DP=140;FS=4.536;MLEAC=1;MLEAF=0.5;MQ=58.17;MQ0=0;MQRankSum=1.542;NEGATIVE_TRAIN_SITE;QD=8.15;ReadPosRankSum=-0.103;SOR=0.269;VQSLOD=-1.496;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:104,36:140:99:1169,0,4245
-chr6	57467282	rs6459264	T	C	1140.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.755;ClippingRankSum=1.153;DB;DP=134;FS=1.319;MLEAC=1;MLEAF=0.5;MQ=58.08;MQ0=0;MQRankSum=1.02;POSITIVE_TRAIN_SITE;QD=8.51;ReadPosRankSum=-0.325;SOR=0.374;VQSLOD=1.58;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:100,34:134:99:1169,0,4245
-chr6	57467303	rs1022846	A	G	3478.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=90;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.14;SOR=5.33;VQSLOD=6.74;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3507,271,0
-chr6	57467317	rs4637646	G	T	1210.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.996;ClippingRankSum=-0.892;DB;DP=73;FS=4.921;MLEAC=1;MLEAF=0.5;MQ=56.76;MQ0=0;MQRankSum=0.26;QD=16.59;ReadPosRankSum=0.593;SOR=0.14;VQSLOD=0.741;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:40,33:73:99:1239,0,1596
-chr6	57467323	rs4424069	G	C	1161.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.993;ClippingRankSum=-0.17;DB;DP=67;FS=4.828;MLEAC=1;MLEAF=0.5;MQ=56.83;MQ0=0;MQRankSum=-0.107;QD=17.34;ReadPosRankSum=0.648;SOR=0.15;VQSLOD=0.857;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:36,31:67:99:1190,0,1431
-chr6	57467456	rs4358625	T	G	43.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=1.27;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:31:72,0,31
-chr6	57472201	rs9885694	A	G	75.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.054;ClippingRankSum=-0.248;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.573;QD=8.42;ReadPosRankSum=1.683;SOR=0.283;VQSLOD=3.58;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:6,3:9:99:104,0,207
-chr6	57472212	rs9296899	T	A	251.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.531;ClippingRankSum=1.531;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.377;QD=22.89;ReadPosRankSum=0.382;SOR=1.802;VQSLOD=4.3;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:3,8:11:88:280,0,88
-chr6	57472255	rs9296900	C	T	533.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.047;ClippingRankSum=-1.484;DB;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.07;MQ0=0;MQRankSum=0.524;POSITIVE_TRAIN_SITE;QD=26.69;ReadPosRankSum=-0.786;SOR=2.093;VQSLOD=5.22;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:5,15:20:99:562,0,141
-chr6	57472299	rs9396358	A	G	360.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.622;ClippingRankSum=0.811;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.59;MQ0=0;MQRankSum=-0.811;QD=10.61;ReadPosRankSum=-1.46;SOR=0.874;VQSLOD=2.75;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:22,12:34:99:389,0,704
-chr6	57472315	rs9296901	A	G	1165.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.692;ClippingRankSum=-0.988;DB;DP=43;FS=2.613;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=0.663;QD=27.11;ReadPosRankSum=-1.151;SOR=0.271;VQSLOD=-0.5021;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:12,31:43:99:1194,0,341
-chr6	57472316	rs9382818	G	A	458.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.993;ClippingRankSum=-0.012;DB;DP=43;FS=2.578;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=-0.36;QD=10.67;ReadPosRankSum=-1.95;SOR=0.156;VQSLOD=0.405;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:26,17:43:99:487,0,974
-chr6	57472344	rs111230027	A	AT	305.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.049;ClippingRankSum=0.23;DB;DP=64;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.71;MQ0=0;MQRankSum=1.887;POSITIVE_TRAIN_SITE;QD=4.78;ReadPosRankSum=-0.919;SOR=0.495;VQSLOD=5.04;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:43,17:60:99:343,0,1062
-chr6	57472476	rs9382819	T	C	344.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.397;ClippingRankSum=1.197;DB;DP=44;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.95;MQ0=0;MQRankSum=-0.718;QD=7.84;ReadPosRankSum=-1.021;SOR=1.226;VQSLOD=1.17;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:30,14:44:99:373,0,1080
-chr6	57472488	rs9382820	C	T	419.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.192;ClippingRankSum=0.268;DB;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.92;MQ0=0;MQRankSum=0.395;QD=9.76;ReadPosRankSum=-1.949;SOR=0.836;VQSLOD=2.8;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:28,15:43:99:448,0,1080
-chr6	57472495	rs62400219	C	G	263.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.265;ClippingRankSum=-0.448;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.78;MQ0=0;MQRankSum=-0.215;QD=6.94;ReadPosRankSum=-0.05;SOR=0.481;VQSLOD=2.66;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:28,10:38:99:292,0,1144
-chr6	57472533	rs9367767	T	C	332.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.122;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.8;MQ0=0;MQRankSum=-0.83;QD=19.57;ReadPosRankSum=0.049;SOR=0.33;VQSLOD=4.65;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:7,10:17:99:361,0,224
-chr6	57472534	rs74369127	T	C	46.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=1.197;ClippingRankSum=0.441;DB;DP=17;FS=7.533;MLEAC=1;MLEAF=0.5;MQ=55.8;MQ0=0;MQRankSum=0.189;NEGATIVE_TRAIN_SITE;QD=2.75;ReadPosRankSum=-1.449;SOR=0.01;VQSLOD=-1.589;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:14,3:17:75:75,0,661
-chr6	57474882	rs62400254	A	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.96;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57474896	rs62400255	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.22;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57476586	rs58187447	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57476608	rs57642151	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57479216	rs4530864	T	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.01;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57482492	rs12197718	T	C	39.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=19.87;SOR=2.303;VQSLOD=6.88;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-chr6	57483749	rs9476179	C	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	57485342	rs9885648	T	C	10.2	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.804;QD=5.1;ReadPosRankSum=0.804;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,1:2:35:38,0,35
-chr6	57485391	rs1853495	T	G	15.65	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=15.65;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	57490861	rs11963269	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57490866	rs9885704	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.81;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57491118	rs9885817	T	C	47.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.98;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:32:76,0,32
-chr6	57492741	rs79386390	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57492762	rs3805807	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57492776	rs77611141	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57493700	rs62404095	T	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.23;SOR=1.609;VQSLOD=6.55;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:6:86,6,0
-chr6	57493709	rs62404096	A	G	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=6.82;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	57493836	rs62404099	C	A	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.43;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57495024	rs5003525	A	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.86;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57495215	rs6939623	T	G	13.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=13.72;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	57495238	rs62404102	T	C	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=5.79;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	57497543	rs6929435	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.11;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57497562	rs76224813	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.26;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57497579	rs73755610	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.63;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57498301	rs11754853	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57498324	rs11759488	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57498894	rs3846934	G	A	268.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.827;ClippingRankSum=0.059;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=-0.884;QD=17.92;ReadPosRankSum=-0.177;SOR=1.112;VQSLOD=4.8;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:6,9:15:99:297,0,200
-chr6	57498944	rs3846935	G	C	516.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.291;ClippingRankSum=-0.826;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=0.064;QD=17.23;ReadPosRankSum=0.233;SOR=0.784;VQSLOD=4.16;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:12,18:30:99:545,0,370
-chr6	57499042	rs5876654	A	AT	87.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.132;ClippingRankSum=-0.57;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=3.51;ReadPosRankSum=-2.324;SOR=0.77;VQSLOD=4.42;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:13,6:19:99:125,0,294
-chr6	57499171	rs3846936	T	C	122.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.731;QD=24.56;ReadPosRankSum=-0.731;SOR=1.981;VQSLOD=4.21;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,4:5:25:151,0,25
-chr6	57499188	rs2151627	C	T	39.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=13.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.9;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:28:68,0,28
-chr6	57499196	rs11423601	C	CA	24.75	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=63.51;MQ0=0;MQRankSum=0.736;QD=8.25;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:27:62,0,27
-chr6	57499926	rs2397610	A	G	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	57500073	rs62404596	G	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=2.303;VQSLOD=6.89;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57500104	rs62404597	G	A	64.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;QD=21.43;SOR=1.179;VQSLOD=6.59;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	57500169	rs6926645	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.37;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57500181	rs76287706	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=4.49;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57500197	rs11329134	GA	G	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.14;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57500204	rs78362714	C	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57500220	rs4537145	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57500442	rs4540266	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57503123	rs2397930	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57503159	rs3857631	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57503199	rs3996830	T	G	35.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.0;QD=8.94;ReadPosRankSum=-1.026;SOR=2.303;VQSLOD=4.04;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:64:64,0,64
-chr6	57503231	rs78058710	A	G	140.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=29.11;SOR=1.609;VQSLOD=4.81;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,4:4:12:168,12,0
-chr6	57503398	rs4995671	C	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.0;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57503441	rs4995670	T	A	94.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;QD=23.69;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.42;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,3:4:33:123,0,33
-chr6	57503444	rs11343070	AC	A	85.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.25;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:1,3:4:33:123,0,33
-chr6	57507333	rs148428624	C	T	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=23.87;SOR=2.303;VQSLOD=6.18;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	57507431	rs139113051	T	C	11.83	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=11.83;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:38,3,0
-chr6	57507846	rs80010809	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57509520	rs62402976	C	T	41.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.87;SOR=0.693;VQSLOD=6.49;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	57511438	rs5011992	G	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=18.25;SOR=0.693;VQSLOD=6.11;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57511528	rs10592385	AATAAC	A	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.58;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=6.31;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57511564	rs5011994	G	A	50.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.58;MQ0=0;QD=25.37;SOR=0.693;VQSLOD=6.78;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	57511607	rs77590924	C	T	14.68	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=70.0;MQ0=0;QD=14.68;SOR=1.609;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	57511894	rs56224263	T	TAC	34.71	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.35;SOR=2.303;VQSLOD=8.87;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
-chr6	57512108	rs6914896	G	A	40.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=4.26;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:2,2:4:69:69,0,71
-chr6	57512340	rs4364484	C	T	502.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.633;ClippingRankSum=-0.142;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.07;MQ0=0;MQRankSum=-1.217;QD=20.11;ReadPosRankSum=-0.311;SOR=1.358;VQSLOD=3.52;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:9,16:25:99:531,0,284
-chr6	57512352	rs5001077	A	T	198.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.659;ClippingRankSum=0.512;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=0.415;QD=6.63;ReadPosRankSum=-0.122;SOR=0.155;VQSLOD=2.84;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:21,8:29:99:227,0,724
-chr6	57512439	rs4294006	T	C	1438.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=3.959;ClippingRankSum=0.864;DB;DP=144;FS=7.438;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-1.071;QD=9.99;ReadPosRankSum=0.578;SOR=0.083;VQSLOD=-0.7791;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:95,49:144:99:1467,0,3234
-chr6	57512476	rs4307164	G	A	5505.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.662;ClippingRankSum=2.077;DB;DP=241;FS=1.012;MLEAC=1;MLEAF=0.5;MQ=58.36;MQ0=0;MQRankSum=1.46;NEGATIVE_TRAIN_SITE;QD=22.85;ReadPosRankSum=-2.015;SOR=0.914;VQSLOD=-1.923;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:78,163:241:99:5534,0,2266
-chr6	57512510	rs4294007	T	G	13853.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=334;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.11;SOR=4.194;VQSLOD=3.16;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,334:334:99:13882,1010,0
-chr6	57512529	rs5001076	C	A	3081.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.175;ClippingRankSum=-2.05;DB;DP=368;FS=3.017;MLEAC=1;MLEAF=0.5;MQ=58.1;MQ0=0;MQRankSum=-0.39;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=0.294;SOR=0.968;VQSLOD=-2.195;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:255,113:368:99:3110,0,8577
-chr6	57512565	rs4294008	T	C	9494.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=5.814;ClippingRankSum=0.828;DB;DP=416;FS=5.007;MLEAC=1;MLEAF=0.5;MQ=57.82;MQ0=0;MQRankSum=2.938;NEGATIVE_TRAIN_SITE;QD=22.82;ReadPosRankSum=-0.668;SOR=1.299;VQSLOD=-2.221;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:138,278:416:99:9523,0,3960
-chr6	57512678	rs4398719	G	A	11124.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=2.677;ClippingRankSum=0.517;DB;DP=458;FS=4.405;MLEAC=1;MLEAF=0.5;MQ=56.48;MQ0=0;MQRankSum=3.775;NEGATIVE_TRAIN_SITE;QD=24.29;ReadPosRankSum=-0.757;SOR=1.082;VQSLOD=-2.409;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:129,325:454:99:11153,0,3458
-chr6	57512711	rs5001484	G	C	5059.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=6.115;ClippingRankSum=-0.961;DB;DP=421;FS=6.509;MLEAC=1;MLEAF=0.5;MQ=53.04;MQ0=0;MQRankSum=1.438;NEGATIVE_TRAIN_SITE;QD=12.02;ReadPosRankSum=0.324;SOR=1.225;VQSLOD=-1.98;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:267,138:405:99:5035,0,6158
-chr6	57512718	rs5001483	T	A	4671.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.87;ClippingRankSum=0.336;DB;DP=406;FS=3.08;MLEAC=1;MLEAF=0.5;MQ=52.12;MQ0=0;MQRankSum=0.364;NEGATIVE_TRAIN_SITE;QD=11.51;ReadPosRankSum=0.365;SOR=1.044;VQSLOD=-1.109;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:274,131:405:99:4700,0,11219
-chr6	57512740	.	CTGTTTT	C	1777.73	VQSRTrancheINDEL99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=0.374;ClippingRankSum=0.035;DP=356;FS=2.783;MLEAC=1;MLEAF=0.5;MQ=49.57;MQ0=0;MQRankSum=-7.25;NEGATIVE_TRAIN_SITE;QD=4.99;ReadPosRankSum=-0.198;SOR=0.328;VQSLOD=-3.212;culprit=DP;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:286,64:350:99:1815,0,11798
-chr6	57512775	rs7773110	T	G	5490.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.254;ClippingRankSum=-0.905;DB;DP=233;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=44.06;MQ0=0;MQRankSum=-4.463;NEGATIVE_TRAIN_SITE;QD=23.57;ReadPosRankSum=-3.464;SOR=1.179;VQSLOD=-2.396;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:92,138:230:99:5519,0,3342
-chr6	57512779	rs76296076	G	T	5369.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.88;ClippingRankSum=-0.404;DB;DP=218;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=42.59;MQ0=0;MQRankSum=-5.088;NEGATIVE_TRAIN_SITE;QD=24.63;ReadPosRankSum=-3.913;SOR=1.132;VQSLOD=-2.613;culprit=ReadPosRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:89,129:218:99:5398,0,3366
-chr6	57512787	.	T	TCACCAAGGC	4709.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=4.158;ClippingRankSum=1.208;DP=186;FS=3.774;MLEAC=1;MLEAF=0.5;MQ=39.95;MQ0=0;MQRankSum=-6.907;QD=25.32;ReadPosRankSum=-2.737;SOR=2.176;VQSLOD=-1.452;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:78,108:186:99:4747,0,3127
-chr6	57512788	.	T	TTA	4547.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.353;ClippingRankSum=-0.603;DP=171;FS=3.354;MLEAC=1;MLEAF=0.5;MQ=40.57;MQ0=0;MQRankSum=-7.416;QD=26.59;ReadPosRankSum=-1.258;SOR=1.878;VQSLOD=-0.9837;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:79,92:171:99:4585,0,3055
-chr6	57512792	rs372064495	T	C	3372.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=7.455;ClippingRankSum=-0.198;DB;DP=157;FS=3.151;MLEAC=1;MLEAF=0.5;MQ=40.8;MQ0=0;MQRankSum=-6.089;NEGATIVE_TRAIN_SITE;QD=21.48;ReadPosRankSum=-0.528;SOR=1.733;VQSLOD=-1.961;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:76,81:157:99:3401,0,3097
-chr6	57512793	rs368894562	AATT	A	3279.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=7.041;ClippingRankSum=-0.005;DB;DP=158;FS=3.066;MLEAC=1;MLEAF=0.5;MQ=41.17;MQ0=0;MQRankSum=-7.628;QD=20.76;ReadPosRankSum=-0.27;SOR=1.67;VQSLOD=-0.929;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:78,80:158:99:3317,0,3097
-chr6	57512825	rs72880943	C	T	1989.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.227;ClippingRankSum=-1.068;DB;DP=102;FS=3.096;MLEAC=1;MLEAF=0.5;MQ=44.73;MQ0=0;MQRankSum=-6.811;NEGATIVE_TRAIN_SITE;QD=19.51;ReadPosRankSum=0.098;SOR=1.704;VQSLOD=-2.269;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:50,52:102:99:2018,0,1929
-chr6	57512826	rs7752845	A	G	1989.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=6.619;ClippingRankSum=1.207;DB;DP=100;FS=3.098;MLEAC=1;MLEAF=0.5;MQ=45.3;MQ0=0;MQRankSum=-6.799;NEGATIVE_TRAIN_SITE;QD=19.9;ReadPosRankSum=0.336;SOR=1.706;VQSLOD=-2.241;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:49,51:100:99:2018,0,1929
-chr6	57512841	rs78256005	A	G	630.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.056;ClippingRankSum=-0.094;DB;DP=79;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=46.16;MQ0=0;MQRankSum=-4.822;NEGATIVE_TRAIN_SITE;QD=7.98;ReadPosRankSum=-1.275;SOR=0.455;VQSLOD=-3.272;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:58,21:79:99:659,0,2392
-chr6	57512850	rs77911716	C	G	547.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=0.371;ClippingRankSum=-0.636;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=46.71;MQ0=0;MQRankSum=-4.402;NEGATIVE_TRAIN_SITE;QD=7.61;ReadPosRankSum=-1.021;SOR=0.357;VQSLOD=-2.865;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:55,17:72:99:576,0,2261
-chr6	57512874	rs71214002	G	A	206.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.499;ClippingRankSum=-0.194;DB;DP=49;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.3;MQ0=0;MQRankSum=-1.846;QD=4.22;ReadPosRankSum=1.072;SOR=0.058;VQSLOD=0.727;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:40,9:49:99:235,0,1573
-chr6	57512889	rs75351177	C	T	149.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.464;ClippingRankSum=-0.226;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.38;MQ0=0;MQRankSum=-2.862;QD=3.94;ReadPosRankSum=-1.167;SOR=0.061;VQSLOD=-0.8131;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:31,7:38:99:178,0,1252
-chr6	57512893	rs77348569	C	T	175.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.044;ClippingRankSum=0.0;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.45;MQ0=0;MQRankSum=-2.215;QD=5.17;ReadPosRankSum=-0.852;SOR=0.078;VQSLOD=0.483;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:27,7:34:99:204,0,1222
-chr6	57512902	rs77563921	G	A	112.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.759;ClippingRankSum=0.9;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.17;MQ0=0;MQRankSum=-1.86;QD=4.03;ReadPosRankSum=-1.14;SOR=0.061;VQSLOD=0.509;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:23,5:28:99:141,0,951
-chr6	57512903	rs75209982	C	A	112.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.939;ClippingRankSum=-1.56;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.17;MQ0=0;MQRankSum=-2.939;QD=4.03;ReadPosRankSum=-1.5;SOR=0.061;VQSLOD=-0.8813;culprit=QD;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:23,5:28:99:141,0,951
-chr6	57512906	rs77519815	T	A	337.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.628;ClippingRankSum=1.732;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.72;MQ0=0;MQRankSum=-3.289;QD=12.51;ReadPosRankSum=-2.536;SOR=0.317;VQSLOD=-0.8036;culprit=MQRankSum;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:17,10:27:99:366,0,726
-chr6	57512916	rs140176282	A	AT	70.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.765;ClippingRankSum=-0.191;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.71;MQ0=0;MQRankSum=-1.244;QD=3.22;ReadPosRankSum=-0.67;SOR=0.039;VQSLOD=4.77;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	0/1:19,3:22:99:108,0,828
-chr6	57513042	rs76730673	C	T	87.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=29.09;SOR=1.179;VQSLOD=6.6;culprit=FS;GENE=PRIM2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:115,9,0
-chr6	57514007	rs4712214	A	G	66.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	57514048	rs79485395	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57517722	rs75802839	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=40.87;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57517733	rs80270590	T	A	96.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.1;MQ0=0;QD=32.09;SOR=2.833;VQSLOD=6.48;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	57517777	rs76191741	A	G	19.81	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.71;MQ0=0;MQRankSum=1.026;QD=3.96;ReadPosRankSum=0.0;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:37:48,0,37
-chr6	57517837	rs79522959	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57517838	rs1853506	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.0;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57517853	rs76412158	A	T	10.9	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.9;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:37,3,0
-chr6	57518157	rs4993255	T	C	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	57519294	rs5017411	C	G	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57519302	rs79076980	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57519303	rs74656916	A	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57519820	rs7744217	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57521340	rs73755643	C	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57521352	rs74795344	A	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.08;SOR=1.609;VQSLOD=6.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:90,6,0
-chr6	57521365	rs76281818	G	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57521370	rs61198018	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.32;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522688	rs76632457	T	C	24.78	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=8.26;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:53,0,33
-chr6	57522722	rs80202467	G	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522729	rs76599881	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522740	rs78027687	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522743	rs72880950	G	A	52.78	PASS	AC=1;AF=0.5;AN=2;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=29.0;MQ0=0;QD=26.39;SOR=0.693;VQSLOD=7.37;culprit=FS	GT:AD:DP:GQ:PL	0/1:0,2:2:26:81,0,26
-chr6	57522745	rs79247610	A	C	52.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.84;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:26:81,0,26
-chr6	57526215	rs5019459	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57526220	rs5019458	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57526231	rs5019457	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57526585	rs62405765	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57526610	rs4370353	C	T	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.16;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57527149	rs77487282	A	C	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57528643	rs4989228	G	A	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	57529061	rs4580853	C	T	46.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=23.37;SOR=0.693;VQSLOD=7.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	57529121	rs4236160	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57531762	rs2894929	A	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.96;MQ0=0;QD=6.2;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57531763	rs4537146	G	A	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.96;MQ0=0;QD=6.2;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57536087	rs77762742	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57536105	rs77828016	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57538839	rs78941520	C	T	43.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=14.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.6;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:72,0,32
-chr6	57538866	rs80259399	C	T	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.77;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,118
-chr6	57538867	rs75525472	A	G	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=4.75;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,118
-chr6	57538878	rs62405823	G	A	86.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;QD=21.69;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.39;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:29:115,0,29
-chr6	57539231	rs73753049	C	T	11.12	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447	GT:AD:DP:GQ:PL	0/1:1,1:2:34:39,0,34
-chr6	57539244	rs77110690	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539245	rs150830310	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539260	rs73753050	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539457	rs62405831	G	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539460	rs35133381	AT	A	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539480	rs2498202	T	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=6.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57544039	rs2498209	C	G	60.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=7.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	57546228	rs12212539	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546230	rs77288943	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.02;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546234	rs12205399	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.35;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546244	rs79029147	C	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.4;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546251	rs78287808	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=32.99;SOR=1.609;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:90,6,0
-chr6	57546252	rs74936228	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=30.52;SOR=1.609;VQSLOD=6.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:90,6,0
-chr6	57546590	rs1853496	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57547418	rs76051348	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57547428	rs76625067	C	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57549247	rs2476489	C	G	16.63	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.63;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	57550746	rs74923423	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57550797	rs78408847	G	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.18;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	57556582	rs2397904	C	T	14.68	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.68;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	57556703	rs2397905	G	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.3;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	57556977	rs113627621	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57556995	rs113330746	A	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57557004	rs4425585	C	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57560942	rs3903831	C	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57560949	rs4097974	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57562969	rs77727649	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57564830	rs78356131	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57564831	rs77336271	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57564861	rs6932761	T	C	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=6.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57565509	rs11965356	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57570509	rs78347797	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57570530	rs6903247	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57574113	rs5008152	G	A	71.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	57574138	rs5008153	T	A	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.43;SOR=1.179;VQSLOD=6.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	57576825	rs73755103	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57576836	rs73755104	T	G	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57576845	rs73755105	C	G	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57595707	rs72871580	T	C	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57595709	rs72871582	C	T	52.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57595723	rs75919230	C	G	83.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.77;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:33:112,0,33
-chr6	57595732	rs72871584	G	T	83.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:33:112,0,33
-chr6	57595770	rs73756249	A	G	34.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.0;QD=8.69;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=4.24;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:37:63,0,37
-chr6	57595781	rs73457550	G	A	33.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.0;QD=8.44;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=3.9;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,2:4:37:62,0,37
-chr6	57595820	rs73756251	T	G	76.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=19.19;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:29:105,0,29
-chr6	57595832	rs77557182	T	C	11.12	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447	GT:AD:DP:GQ:PL	0/1:1,1:2:39:39,0,39
-chr6	57595845	rs76008427	A	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57597257	rs72871594	A	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=7.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	57597260	rs72871595	A	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=30.27;SOR=1.609;VQSLOD=6.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:79,6,0
-chr6	57603832	rs80257130	A	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57603839	rs147344208	A	AT	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57603845	rs72873407	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57606933	rs73757604	T	C	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57606965	rs74644238	T	G	66.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	57606996	rs73459287	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57607035	rs73757606	G	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57607044	rs73757607	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57607068	rs72873457	C	T	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57607074	rs4360139	G	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57608079	rs73459299	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57612661	.	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57618295	rs5876690	G	GA	25.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.86;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:62,6,0
-chr6	57673397	rs7765475	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57686962	rs140945786	G	T	100.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.55;POSITIVE_TRAIN_SITE;QD=14.4;ReadPosRankSum=0.937;SOR=3.221;VQSLOD=0.651;culprit=FS;GENE=GAPDHP41	GT:AD:DP:GQ:PL	0/1:3,4:7:99:129,0,102
-chr6	57699097	rs6459305	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57710858	rs149357140	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57711844	rs143767848	A	T	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=8.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	57723952	rs11295509	CA	C	37.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.42;SOR=1.179;VQSLOD=5.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:74,9,0
-chr6	57732063	.	C	A	12.13	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=3.03;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:17:40,0,17
-chr6	57737999	rs142093663	G	A	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=27.87;SOR=0.693;VQSLOD=6.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	57738613	.	C	T	20.78	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	57785184	rs116169256	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57826827	.	TA	T	24.72	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.24;MQ0=0;QD=12.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	57841273	rs188364530	C	T	1364.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.628;ClippingRankSum=0.296;DB;DP=85;FS=7.134;MLEAC=1;MLEAF=0.5;MQ=59.34;MQ0=0;MQRankSum=1.622;POSITIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-0.11;SOR=0.843;VQSLOD=1.24;culprit=FS;GENE=RBBP4P3	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1393,0,1205
-chr6	57841320	rs140816261	G	T	1315.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.878;ClippingRankSum=-0.287;DB;DP=83;FS=5.67;MLEAC=1;MLEAF=0.5;MQ=57.34;MQ0=0;MQRankSum=-0.132;POSITIVE_TRAIN_SITE;QD=15.85;ReadPosRankSum=-0.515;SOR=1.312;VQSLOD=1.62;culprit=FS;GENE=RBBP4P3	GT:AD:DP:GQ:PL	0/1:40,43:83:99:1344,0,1358
-chr6	57841627	rs149540211	AC	A	954.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.085;ClippingRankSum=0.306;DB;DP=80;FS=3.046;MLEAC=1;MLEAF=0.5;MQ=59.31;MQ0=0;MQRankSum=1.819;QD=11.93;ReadPosRankSum=-1.129;SOR=0.798;VQSLOD=0.74;culprit=MQRankSum;GENE=RBBP4P3	GT:AD:DP:GQ:PL	0/1:42,36:78:99:992,0,1172
-chr6	57842518	rs149985050	G	T	70.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.0;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=10.11;ReadPosRankSum=0.937;SOR=0.495;VQSLOD=5.83;culprit=FS;GENE=RBBP4P3	GT:AD:DP:GQ:PL	0/1:4,3:7:99:99,0,144
-chr6	57843574	rs115026909	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57857856	rs3000344	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.19;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57972306	rs55752203	TG	T	24.72	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=12.36;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	57977600	rs115553313	C	T	97.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=1.179;VQSLOD=8.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:125,9,0
-chr6	57977640	rs4960490	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57998262	rs9476413	T	C	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=6.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	58028492	rs147632909	C	A	37.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=9.44;ReadPosRankSum=0.0;SOR=2.303;VQSLOD=5.34;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:66:66,0,74
-chr6	58039789	rs9382925	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58165037	.	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	58165039	.	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.45;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	58165065	.	GT	G	53.7	PASS	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	58173632	rs114670858	T	G	20.78	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	58246055	rs6918567	T	C	2357.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.591;ClippingRankSum=-0.427;DB;DP=249;FS=6.315;MLEAC=1;MLEAF=0.5;MQ=50.51;MQ0=0;MQRankSum=-11.921;POSITIVE_TRAIN_SITE;QD=9.47;ReadPosRankSum=2.161;SOR=1.112;VQSLOD=-3.174;culprit=MQRankSum;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:179,69:248:99:2386,0,8176
-chr6	58246056	rs6930828	G	A	2357.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.659;ClippingRankSum=0.056;DB;DP=250;FS=5.251;MLEAC=1;MLEAF=0.5;MQ=50.59;MQ0=0;MQRankSum=-11.878;QD=9.43;ReadPosRankSum=-0.007;SOR=1.079;VQSLOD=-4.553;culprit=MQRankSum;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:179,70:249:99:2386,0,8176
-chr6	58246143	rs6931014	G	A	3997.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.856;ClippingRankSum=-0.73;DB;DP=326;FS=0.849;MLEAC=1;MLEAF=0.5;MQ=49.42;MQ0=0;MQRankSum=-4.926;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=3.641;SOR=0.631;VQSLOD=-1.659;culprit=MQRankSum;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:186,138:324:99:4026,0,5840
-chr6	58250570	rs9500243	A	T	402.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.537;ClippingRankSum=0.754;DB;DP=40;FS=8.709;MLEAC=1;MLEAF=0.5;MQ=50.1;MQ0=0;MQRankSum=0.698;POSITIVE_TRAIN_SITE;QD=10.07;ReadPosRankSum=0.112;SOR=0.032;VQSLOD=1.36;culprit=FS;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:25,15:40:99:431,0,789
-chr6	58252949	.	A	G	37.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.322;ClippingRankSum=-0.684;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=36.3;MQ0=0;MQRankSum=-0.684;QD=4.72;ReadPosRankSum=0.322;SOR=0.368;VQSLOD=3.52;culprit=QD;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:5,3:8:66:66,0,144
-chr6	58260059	rs74657950	G	A	177.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.067;ClippingRankSum=0.058;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.79;MQ0=0;MQRankSum=-2.025;QD=11.85;ReadPosRankSum=0.984;SOR=0.582;VQSLOD=2.97;culprit=FS;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:8,7:15:99:206,0,240
-chr6	58260138	rs62464086	A	G	246.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.547;ClippingRankSum=-0.921;DB;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-2.308;QD=5.74;ReadPosRankSum=0.921;SOR=0.569;VQSLOD=0.439;culprit=QD;GENE=GUSBP4	GT:AD:DP:GQ:PL	0/1:28,14:42:99:275,0,785
-chr6	58263609	rs4079740	A	G	17.84	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=44.65;MQ0=0;MQRankSum=-1.231;QD=3.57;ReadPosRankSum=0.358;SOR=0.446;GENE=GUSBP4,POM121L14P	GT:AD:DP:GQ:PL	0/1:3,2:5:46:46,0,99
-chr6	58263871	rs6588681	T	C	325.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.892;ClippingRankSum=-0.055;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.21;MQ0=0;MQRankSum=-2.022;QD=9.87;ReadPosRankSum=1.73;SOR=0.941;VQSLOD=1.68;culprit=FS;GENE=POM121L14P	GT:AD:DP:GQ:PL	0/1:19,14:33:99:354,0,577
-chr6	58263932	rs1810425	G	A	548.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.642;ClippingRankSum=-0.644;DB;DP=42;FS=1.298;MLEAC=1;MLEAF=0.5;MQ=56.18;MQ0=0;MQRankSum=-0.407;QD=13.07;ReadPosRankSum=-0.223;SOR=1.002;VQSLOD=1.43;culprit=FS;GENE=POM121L14P	GT:AD:DP:GQ:PL	0/1:23,18:41:99:577,0,758
-chr6	58263952	rs1810426	A	G	478.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.162;ClippingRankSum=-0.058;DB;DP=46;FS=2.893;MLEAC=1;MLEAF=0.5;MQ=56.38;MQ0=0;MQRankSum=1.471;QD=10.41;ReadPosRankSum=0.683;SOR=1.251;VQSLOD=1.23;culprit=QD;GENE=POM121L14P	GT:AD:DP:GQ:PL	0/1:27,18:45:99:507,0,927
-chr6	58265128	rs9391382	T	C	346.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=1.844;ClippingRankSum=-0.596;DB;DP=54;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=43.99;MQ0=0;MQRankSum=-5.275;NEGATIVE_TRAIN_SITE;QD=6.42;ReadPosRankSum=-1.037;SOR=0.793;VQSLOD=-3.62;culprit=MQRankSum;GENE=POM121L14P	GT:AD:DP:GQ:PL	0/1:36,18:54:99:375,0,1179
-chr6	58265398	rs17488291	G	A	1245.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.662;ClippingRankSum=0.505;DB;DP=89;FS=7.385;MLEAC=1;MLEAF=0.5;MQ=53.47;MQ0=0;MQRankSum=-1.229;POSITIVE_TRAIN_SITE;QD=14.0;ReadPosRankSum=1.648;SOR=1.478;VQSLOD=1.83;culprit=FS;GENE=POM121L14P	GT:AD:DP:GQ:PL	0/1:47,42:89:99:1274,0,1450
-chr6	58265469	.	G	GTTT	400.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.047;ClippingRankSum=1.203;DP=68;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.92;MQ0=0;MQRankSum=-3.451;QD=5.89;ReadPosRankSum=-0.359;SOR=0.651;VQSLOD=1.97;culprit=FS;GENE=POM121L14P	GT:AD:DP:GQ:PL	0/1:34,19:53:99:438,0,1230
-chr6	58273526	rs4928423	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.0;MQ0=0;QD=10.88;SOR=0.693;GENE=LINC00680	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58287821	rs9404620	A	G	128.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.307;ClippingRankSum=0.876;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.39;MQ0=0;MQRankSum=0.729;POSITIVE_TRAIN_SITE;QD=14.31;ReadPosRankSum=0.0;SOR=0.892;VQSLOD=6.42;culprit=FS;GENE=LINC00680	GT:AD:DP:GQ:PL	0/1:4,5:9:99:157,0,118
-chr6	58294828	rs2012049	C	T	129.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.663;ClippingRankSum=-0.251;DB;DP=17;FS=2.884;MLEAC=1;MLEAF=0.5;MQ=51.67;MQ0=0;MQRankSum=-2.161;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=-0.151;SOR=1.688;VQSLOD=0.937;culprit=QD;GENE=GAPDHP15	GT:AD:DP:GQ:PL	0/1:11,6:17:99:158,0,414
-chr6	58302194	rs693484	T	A	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	58365506	rs60186309	T	TA	41.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.85;SOR=0.693;VQSLOD=8.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	58447068	rs1224740	A	G	1017.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.8;ClippingRankSum=-0.222;DB;DP=64;FS=3.511;MLEAC=1;MLEAF=0.5;MQ=58.23;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=15.9;ReadPosRankSum=-0.356;SOR=1.296;VQSLOD=3.1;culprit=ReadPosRankSum;GENE=RBBP4P4	GT:AD:DP:GQ:PL	0/1:32,32:64:99:1046,0,1021
-chr6	58465552	rs1224802	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=22.51;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58490384	rs7770844	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58693830	rs2343003	A	C	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	58735978	rs2343014	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58776289	rs4357163	T	G	186.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.202;ClippingRankSum=0.775;DB;DP=26;FS=2.192;MLEAC=1;MLEAF=0.5;MQ=33.3;MQ0=0;MQRankSum=-1.085;QD=7.18;ReadPosRankSum=0.837;SOR=1.46;VQSLOD=0.168;culprit=QD	GT:AD:DP:GQ:PL	0/1:13,10:23:99:215,0,418
-chr6	58776318	rs9986349	A	G	261.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.368;ClippingRankSum=-0.152;DB;DP=22;FS=2.098;MLEAC=1;MLEAF=0.5;MQ=32.68;MQ0=0;MQRankSum=-0.684;QD=11.9;ReadPosRankSum=-0.304;SOR=0.243;VQSLOD=1.18;culprit=QD	GT:AD:DP:GQ:PL	0/1:11,9:20:99:290,0,435
-chr6	58776319	rs9638012	C	T	871.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=22;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=32.68;MQ0=0;QD=28.76;SOR=2.093;VQSLOD=5.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,20:20:60:900,60,0
-chr6	58776352	rs4317432	T	C	267.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.799;ClippingRankSum=-0.318;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=32.04;MQ0=0;MQRankSum=-0.847;QD=15.75;ReadPosRankSum=-1.059;SOR=0.653;VQSLOD=4.28;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,9:16:99:296,0,314
-chr6	58776411	rs9638013	A	G	364.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.887;ClippingRankSum=-1.415;DB;DP=18;FS=2.846;MLEAC=1;MLEAF=0.5;MQ=28.44;MQ0=0;MQRankSum=-0.283;QD=20.26;ReadPosRankSum=0.962;SOR=0.148;VQSLOD=1.19;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,13:17:99:393,0,132
-chr6	58776442	rs9638019	T	C	491.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.786;ClippingRankSum=0.381;DB;DP=25;FS=2.593;MLEAC=1;MLEAF=0.5;MQ=35.87;MQ0=0;MQRankSum=-0.498;QD=19.67;ReadPosRankSum=0.088;SOR=1.863;VQSLOD=1.35;culprit=QD	GT:AD:DP:GQ:PL	0/1:10,14:24:99:520,0,292
-chr6	58776542	rs4524636	G	A	45.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.367;ClippingRankSum=0.115;DB;DP=64;FS=1.496;MLEAC=1;MLEAF=0.5;MQ=48.96;MQ0=0;MQRankSum=0.136;NEGATIVE_TRAIN_SITE;QD=0.72;ReadPosRankSum=-0.073;SOR=1.179;VQSLOD=-1.126;culprit=QD	GT:AD:DP:GQ:PL	0/1:54,8:62:74:74,0,1805
-chr6	58776555	rs4928523	T	C	742.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.227;ClippingRankSum=-0.403;DB;DP=63;FS=9.224;MLEAC=1;MLEAF=0.5;MQ=49.77;MQ0=0;MQRankSum=0.433;QD=11.79;ReadPosRankSum=1.884;SOR=1.229;VQSLOD=0.004;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,25:61:99:771,0,1202
-chr6	58776592	rs9377908	A	G	222.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.65;ClippingRankSum=-0.434;DB;DP=74;FS=1.153;MLEAC=1;MLEAF=0.5;MQ=54.28;MQ0=0;MQRankSum=0.889;NEGATIVE_TRAIN_SITE;QD=3.01;ReadPosRankSum=0.918;SOR=0.46;VQSLOD=-0.9187;culprit=QD	GT:AD:DP:GQ:PL	0/1:58,14:72:99:251,0,2116
-chr6	58776745	rs9632507	C	T	3168.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=80;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.29;MQ0=0;QD=32.18;SOR=0.927;VQSLOD=5.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3197,226,0
-chr6	58776782	rs9632508	A	T	3215.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=83;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.76;MQ0=0;QD=30.1;SOR=0.887;VQSLOD=5.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3244,240,0
-chr6	58776802	rs4401693	T	G	670.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.16;ClippingRankSum=-0.171;DB;DP=80;FS=3.349;MLEAC=1;MLEAF=0.5;MQ=54.82;MQ0=0;MQRankSum=2.069;QD=8.38;ReadPosRankSum=0.137;SOR=1.112;VQSLOD=-0.5951;culprit=QD	GT:AD:DP:GQ:PL	0/1:49,25:74:99:699,0,1658
-chr6	58776855	rs4928552	A	G	1233.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.182;ClippingRankSum=0.37;DB;DP=79;FS=1.923;MLEAC=1;MLEAF=0.5;MQ=54.95;MQ0=0;MQRankSum=1.187;QD=15.62;ReadPosRankSum=-0.469;SOR=0.872;VQSLOD=1.36;culprit=DP	GT:AD:DP:GQ:PL	0/1:35,38:73:99:1262,0,1231
-chr6	58776887	rs113904338	A	G	105.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=3.374;ClippingRankSum=-1.479;DB;DP=74;FS=1.493;MLEAC=1;MLEAF=0.5;MQ=54.73;MQ0=0;MQRankSum=1.286;NEGATIVE_TRAIN_SITE;QD=1.43;ReadPosRankSum=1.305;SOR=1.159;VQSLOD=-1.368;culprit=QD	GT:AD:DP:GQ:PL	0/1:59,8:67:99:134,0,2069
-chr6	58776958	rs4562168	A	T	38.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.772;ClippingRankSum=1.153;DB;DP=68;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.56;MQ0=0;MQRankSum=0.582;QD=0.57;ReadPosRankSum=1.725;SOR=0.941;VQSLOD=0.88;culprit=QD	GT:AD:DP:GQ:PL	0/1:58,7:65:67:67,0,2198
-chr6	58776965	rs9632509	C	T	18.82	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.964;ClippingRankSum=-1.381;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.35;MQ0=0;MQRankSum=1.202;QD=0.26;ReadPosRankSum=1.441;SOR=0.796	GT:AD:DP:GQ:PL	0/1:62,7:69:47:47,0,2234
-chr6	58776982	rs9632510	G	T	1497.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.267;ClippingRankSum=0.065;DB;DP=67;FS=1.041;MLEAC=1;MLEAF=0.5;MQ=51.72;MQ0=0;MQRankSum=-0.411;QD=22.35;ReadPosRankSum=-0.887;SOR=0.51;VQSLOD=-0.2878;culprit=FS	GT:AD:DP:GQ:PL	0/1:19,46:65:99:1526,0,547
-chr6	58776984	rs56092323	A	T	39.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.0;ClippingRankSum=0.603;DB;DP=67;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.72;MQ0=0;MQRankSum=1.386;QD=0.59;ReadPosRankSum=1.323;SOR=0.787;VQSLOD=0.978;culprit=QD	GT:AD:DP:GQ:PL	0/1:58,7:65:68:68,0,2352
-chr6	58777039	rs28781680	G	A	376.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.782;ClippingRankSum=-0.924;DB;DP=63;FS=4.123;MLEAC=1;MLEAF=0.5;MQ=46.06;MQ0=0;MQRankSum=1.682;QD=5.98;ReadPosRankSum=-0.766;SOR=1.179;VQSLOD=-0.5013;culprit=QD	GT:AD:DP:GQ:PL	0/1:47,16:63:99:405,0,1853
-chr6	58777056	rs9654654	G	T	772.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.293;ClippingRankSum=0.839;DB;DP=64;FS=5.15;MLEAC=1;MLEAF=0.5;MQ=45.93;MQ0=0;MQRankSum=1.899;QD=12.07;ReadPosRankSum=-0.041;SOR=1.004;VQSLOD=0.153;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:39,25:64:99:801,0,1404
-chr6	58777074	rs4388312	C	T	822.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.624;ClippingRankSum=-1.281;DB;DP=65;FS=6.614;MLEAC=1;MLEAF=0.5;MQ=49.69;MQ0=0;MQRankSum=0.164;QD=12.66;ReadPosRankSum=-1.018;SOR=0.612;VQSLOD=0.293;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,31:65:99:851,0,1154
-chr6	58777106	rs4610595	A	G	643.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.791;ClippingRankSum=1.422;DB;DP=67;FS=5.024;MLEAC=1;MLEAF=0.5;MQ=56.66;MQ0=0;MQRankSum=-0.611;QD=9.61;ReadPosRankSum=0.573;SOR=0.565;VQSLOD=0.035;culprit=QD	GT:AD:DP:GQ:PL	0/1:41,26:67:99:672,0,1465
-chr6	58777109	rs9647639	C	T	510.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.158;ClippingRankSum=0.783;DB;DP=69;FS=9.064;MLEAC=1;MLEAF=0.5;MQ=57.11;MQ0=0;MQRankSum=0.783;NEGATIVE_TRAIN_SITE;QD=7.4;ReadPosRankSum=-1.203;SOR=1.679;VQSLOD=-1.89;culprit=QD	GT:AD:DP:GQ:PL	0/1:46,23:69:99:539,0,1603
-chr6	58777156	rs4577825	C	G	121.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.79;ClippingRankSum=0.33;DB;DP=81;FS=4.661;MLEAC=1;MLEAF=0.5;MQ=57.6;MQ0=0;MQRankSum=1.12;NEGATIVE_TRAIN_SITE;QD=1.5;ReadPosRankSum=-0.258;SOR=1.196;VQSLOD=-2.068;culprit=QD	GT:AD:DP:GQ:PL	0/1:67,11:78:99:150,0,2400
-chr6	58777178	rs9638022	G	T	2960.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.64;MQ0=0;QD=28.06;SOR=0.774;VQSLOD=5.1;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2989,229,0
-chr6	58777233	rs4336468	C	T	554.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.43;ClippingRankSum=-1.64;DB;DP=65;FS=1.047;MLEAC=1;MLEAF=0.5;MQ=57.82;MQ0=0;MQRankSum=0.052;QD=8.53;ReadPosRankSum=0.696;SOR=0.914;VQSLOD=0.514;culprit=QD	GT:AD:DP:GQ:PL	0/1:44,19:63:99:583,0,1593
-chr6	58777237	rs4518527	A	G	633.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.144;ClippingRankSum=0.639;DB;DP=59;FS=5.406;MLEAC=1;MLEAF=0.5;MQ=58.17;MQ0=0;MQRankSum=1.634;QD=10.74;ReadPosRankSum=-0.971;SOR=0.569;VQSLOD=-0.0454;culprit=QD	GT:AD:DP:GQ:PL	0/1:34,24:58:99:662,0,1277
-chr6	58777276	rs4446588	A	C	897.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.1;ClippingRankSum=0.236;DB;DP=62;FS=0.99;MLEAC=1;MLEAF=0.5;MQ=57.73;MQ0=0;MQRankSum=1.879;QD=14.48;ReadPosRankSum=0.023;SOR=0.662;VQSLOD=0.954;culprit=FS	GT:AD:DP:GQ:PL	0/1:32,27:59:99:926,0,946
-chr6	58777295	rs9638023	T	C	2798.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=67;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.73;MQ0=0;QD=33.48;SOR=0.79;VQSLOD=5.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2827,196,0
-chr6	58777312	rs9632511	T	C	759.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=0.614;ClippingRankSum=-1.05;DB;DP=72;FS=11.531;MLEAC=1;MLEAF=0.5;MQ=57.36;MQ0=0;MQRankSum=-1.776;QD=10.55;ReadPosRankSum=0.984;SOR=1.631;VQSLOD=-1.664;culprit=FS	GT:AD:DP:GQ:PL	0/1:44,23:67:99:788,0,1478
-chr6	58777366	rs9632513	A	G	2731.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=68;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.45;MQ0=0;QD=29.84;SOR=0.756;VQSLOD=5.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2760,199,0
-chr6	58777546	rs9632515	G	A	2432.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.61;MQ0=0;QD=30.91;SOR=0.723;VQSLOD=5.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,67:67:99:2461,201,0
-chr6	58777573	rs9632516	C	T	2295.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.0;AN=2;BaseQRankSum=-0.251;ClippingRankSum=1.138;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.3;MQ0=0;MQRankSum=-0.559;NEGATIVE_TRAIN_SITE;QD=34.78;ReadPosRankSum=1.794;SOR=0.826;VQSLOD=-0.6277;culprit=QD	GT:AD:DP:GQ:PL	1/1:2,62:64:99:2324,117,0
-chr6	58777583	rs4351287	A	G	250.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.157;ClippingRankSum=0.238;DB;DP=69;FS=1.199;MLEAC=1;MLEAF=0.5;MQ=55.52;MQ0=0;MQRankSum=-0.221;QD=3.63;ReadPosRankSum=0.648;SOR=0.717;VQSLOD=-0.7794;culprit=QD	GT:AD:DP:GQ:PL	0/1:52,13:65:99:279,0,1731
-chr6	58777599	.	T	G	144.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=0.474;ClippingRankSum=-0.957;DP=71;FS=5.022;MLEAC=1;MLEAF=0.5;MQ=57.05;MQ0=0;MQRankSum=-0.563;NEGATIVE_TRAIN_SITE;QD=2.04;ReadPosRankSum=-0.063;SOR=0.899;VQSLOD=-1.822;culprit=QD	GT:AD:DP:GQ:PL	0/1:56,10:66:99:173,0,1929
-chr6	58777775	.	A	C	471.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.3;ClippingRankSum=0.625;DP=64;FS=1.059;MLEAC=1;MLEAF=0.5;MQ=56.1;MQ0=0;MQRankSum=0.17;QD=7.37;ReadPosRankSum=1.517;SOR=0.904;VQSLOD=0.168;culprit=QD	GT:AD:DP:GQ:PL	0/1:40,19:59:99:500,0,1465
-chr6	58777789	rs4296911	T	C	850.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.376;ClippingRankSum=-0.201;DB;DP=67;FS=8.737;MLEAC=1;MLEAF=0.5;MQ=55.92;MQ0=0;MQRankSum=0.892;QD=12.7;ReadPosRankSum=-2.082;SOR=0.733;VQSLOD=-0.2447;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:35,28:63:99:879,0,1323
-chr6	58777828	rs11211786	G	A	652.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.463;ClippingRankSum=-0.018;DB;DP=77;FS=10.707;MLEAC=1;MLEAF=0.5;MQ=55.75;MQ0=0;MQRankSum=2.081;NEGATIVE_TRAIN_SITE;QD=8.48;ReadPosRankSum=-0.651;SOR=1.322;VQSLOD=-1.674;culprit=QD	GT:AD:DP:GQ:PL	0/1:46,26:72:99:681,0,1420
-chr6	58777836	rs9632517	A	C	2870.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=76;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.16;MQ0=0;QD=28.37;SOR=0.811;VQSLOD=2.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2899,214,0
-chr6	58777939	rs9632518	G	A	2463.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=65;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.89;MQ0=0;QD=25.14;SOR=1.143;VQSLOD=4.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2492,187,0
-chr6	58777952	rs4546514	A	G	853.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.23;ClippingRankSum=-1.282;DB;DP=63;FS=2.122;MLEAC=1;MLEAF=0.5;MQ=43.01;MQ0=0;MQRankSum=1.134;QD=13.55;ReadPosRankSum=2.245;SOR=0.46;VQSLOD=1.24;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:28,32:60:99:882,0,851
-chr6	58778001	.	G	A	533.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.458;ClippingRankSum=-0.8;DP=68;FS=0.981;MLEAC=1;MLEAF=0.5;MQ=45.56;MQ0=0;MQRankSum=-0.598;QD=7.85;ReadPosRankSum=0.699;SOR=0.563;VQSLOD=-0.063;culprit=QD	GT:AD:DP:GQ:PL	0/1:41,22:63:99:562,0,1296
-chr6	58778019	rs9638027	T	G	165.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.004;ClippingRankSum=-1.301;DB;DP=72;FS=1.422;MLEAC=1;MLEAF=0.5;MQ=45.92;MQ0=0;MQRankSum=1.339;NEGATIVE_TRAIN_SITE;QD=2.3;ReadPosRankSum=0.522;SOR=1.106;VQSLOD=-1.041;culprit=QD	GT:AD:DP:GQ:PL	0/1:56,9:65:99:194,0,2191
-chr6	58778025	rs9638028	A	G	2317.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.876;ClippingRankSum=-0.113;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.27;MQ0=0;MQRankSum=-0.523;QD=32.19;ReadPosRankSum=0.277;SOR=0.604;VQSLOD=0.716;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,60:67:99:2346,0,110
-chr6	58778036	rs9404685	A	C	534.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.105;ClippingRankSum=-1.103;DB;DP=69;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=44.49;MQ0=0;MQRankSum=-0.499;QD=7.75;ReadPosRankSum=1.173;SOR=0.668;VQSLOD=2.83;culprit=QD	GT:AD:DP:GQ:PL	0/1:38,25:63:99:563,0,1164
-chr6	58778039	rs9638014	G	C	2754.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.01;MQ0=0;QD=30.33;SOR=0.79;VQSLOD=5.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2783,190,0
-chr6	58778081	rs4389792	T	G	2804.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.55;MQ0=0;QD=36.83;SOR=0.865;VQSLOD=3.57;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2833,190,0
-chr6	58778082	rs4346876	T	C	2759.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.55;MQ0=0;QD=35.85;SOR=0.865;VQSLOD=5.04;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2788,187,0
-chr6	58778100	rs9391506	A	T	94.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.077;ClippingRankSum=-0.536;DB;DP=63;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.08;MQ0=0;MQRankSum=-0.098;QD=1.5;ReadPosRankSum=-0.93;SOR=0.801;VQSLOD=0.858;culprit=QD	GT:AD:DP:GQ:PL	0/1:48,9:57:99:123,0,1551
-chr6	58778108	rs4308591	G	C	2796.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=68;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.2;MQ0=0;QD=21.44;SOR=1.092;VQSLOD=3.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2825,196,0
-chr6	58778145	rs9500568	T	C	228.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=1.501;ClippingRankSum=0.435;DB;DP=69;FS=1.229;MLEAC=1;MLEAF=0.5;MQ=55.74;MQ0=0;MQRankSum=0.074;QD=3.32;ReadPosRankSum=0.631;SOR=0.425;VQSLOD=-0.7171;culprit=QD	GT:AD:DP:GQ:PL	0/1:52,13:65:99:257,0,1648
-chr6	58778148	rs12213271	T	C	43.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.529;ClippingRankSum=0.21;DB;DP=69;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.74;MQ0=0;MQRankSum=-2.466;NEGATIVE_TRAIN_SITE;QD=0.63;ReadPosRankSum=-1.168;SOR=0.796;VQSLOD=-1.747;culprit=QD	GT:AD:DP:GQ:PL	0/1:57,8:65:72:72,0,1899
-chr6	58778190	rs9767581	T	G	325.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.002;ClippingRankSum=-0.571;DB;DP=71;FS=1.103;MLEAC=1;MLEAF=0.5;MQ=57.28;MQ0=0;MQRankSum=0.86;QD=4.59;ReadPosRankSum=0.34;SOR=0.886;VQSLOD=-0.4734;culprit=QD	GT:AD:DP:GQ:PL	0/1:52,16:68:99:354,0,1641
-chr6	58778207	rs6588729	G	A	2273.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.0;AN=2;BaseQRankSum=1.676;ClippingRankSum=-1.397;DB;DP=65;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.24;MQ0=0;MQRankSum=0.95;NEGATIVE_TRAIN_SITE;QD=34.98;ReadPosRankSum=-1.341;SOR=0.236;VQSLOD=-1.078;culprit=QD	GT:AD:DP:GQ:PL	1/1:1,61:62:99:2302,182,0
-chr6	58778244	rs6588730	A	T	2044.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=65;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.41;MQ0=0;QD=31.46;SOR=0.76;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2073,180,0
-chr6	58778404	rs6588731	C	A	2347.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=57;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.8;MQ0=0;QD=32.04;SOR=0.808;VQSLOD=5.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,53:53:99:2376,160,0
-chr6	58778405	rs6588732	C	T	2392.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=56;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.66;MQ0=0;QD=27.48;SOR=0.77;VQSLOD=4.38;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2421,163,0
-chr6	58778412	rs6588733	T	C	2705.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=62;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.42;MQ0=0;QD=34.01;SOR=0.762;VQSLOD=5.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2734,184,0
-chr6	58778452	rs4928629	A	C	970.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.809;ClippingRankSum=-0.744;DB;DP=64;FS=5.099;MLEAC=1;MLEAF=0.5;MQ=55.54;MQ0=0;MQRankSum=2.13;POSITIVE_TRAIN_SITE;QD=15.17;ReadPosRankSum=1.163;SOR=1.249;VQSLOD=1.86;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:29,32:61:99:999,0,986
-chr6	58778456	.	G	T	154.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.779;ClippingRankSum=-0.534;DP=68;FS=2.839;MLEAC=1;MLEAF=0.5;MQ=55.81;MQ0=0;MQRankSum=1.216;NEGATIVE_TRAIN_SITE;QD=2.28;ReadPosRankSum=0.079;SOR=0.654;VQSLOD=-0.8069;culprit=QD	GT:AD:DP:GQ:PL	0/1:54,11:65:99:183,0,2074
-chr6	58778482	rs6588734	G	A	2628.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=64;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.61;MQ0=0;QD=31.77;SOR=0.906;VQSLOD=3.8;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2657,190,0
-chr6	58778519	rs4928633	A	G	847.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.545;ClippingRankSum=-1.803;DB;DP=75;FS=6.752;MLEAC=1;MLEAF=0.5;MQ=54.72;MQ0=0;MQRankSum=-1.213;QD=11.3;ReadPosRankSum=0.443;SOR=1.183;VQSLOD=-0.4825;culprit=FS	GT:AD:DP:GQ:PL	0/1:44,24:68:99:876,0,1700
-chr6	58778530	rs9647643	T	C	919.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=3.069;ClippingRankSum=-0.13;DB;DP=71;FS=8.855;MLEAC=1;MLEAF=0.5;MQ=54.76;MQ0=0;MQRankSum=-0.936;QD=12.95;ReadPosRankSum=-0.567;SOR=1.363;VQSLOD=-0.0751;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,26:64:99:948,0,1688
-chr6	58778531	rs9647644	A	C	922.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.99;ClippingRankSum=0.934;DB;DP=70;FS=8.966;MLEAC=1;MLEAF=0.5;MQ=54.68;MQ0=0;MQRankSum=-1.454;QD=13.18;ReadPosRankSum=-0.204;SOR=1.572;VQSLOD=-0.337;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,25:63:99:951,0,1651
-chr6	58778577	rs6588735	T	A	348.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.086;ClippingRankSum=0.432;DB;DP=70;FS=8.999;MLEAC=1;MLEAF=0.5;MQ=54.75;MQ0=0;MQRankSum=-0.934;NEGATIVE_TRAIN_SITE;QD=4.98;ReadPosRankSum=0.225;SOR=0.956;VQSLOD=-2.51;culprit=QD	GT:AD:DP:GQ:PL	0/1:49,13:62:99:377,0,2028
-chr6	58778584	rs6588736	T	G	310.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.597;ClippingRankSum=0.859;DB;DP=67;FS=2.94;MLEAC=1;MLEAF=0.5;MQ=54.51;MQ0=0;MQRankSum=0.896;QD=4.64;ReadPosRankSum=0.545;SOR=0.275;VQSLOD=-0.1432;culprit=QD	GT:AD:DP:GQ:PL	0/1:48,12:60:99:339,0,2037
-chr6	58778664	rs112323615	T	G	597.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.932;ClippingRankSum=-0.755;DB;DP=68;FS=5.051;MLEAC=1;MLEAF=0.5;MQ=57.08;MQ0=0;MQRankSum=0.959;QD=8.79;ReadPosRankSum=-0.864;SOR=0.98;VQSLOD=-0.2673;culprit=QD	GT:AD:DP:GQ:PL	0/1:44,22:66:99:626,0,1333
-chr6	58778716	rs7453620	A	C	1189.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.027;ClippingRankSum=-0.97;DB;DP=79;FS=6.175;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=-0.769;QD=15.06;ReadPosRankSum=-1.098;SOR=0.261;VQSLOD=0.195;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,39:75:99:1218,0,1070
-chr6	58778747	rs12214947	T	C	88.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.524;ClippingRankSum=-1.054;DB;DP=88;FS=4.622;MLEAC=1;MLEAF=0.5;MQ=58.67;MQ0=0;MQRankSum=0.705;NEGATIVE_TRAIN_SITE;QD=1.01;ReadPosRankSum=1.189;SOR=0.575;VQSLOD=-2.375;culprit=QD	GT:AD:DP:GQ:PL	0/1:72,11:83:99:117,0,2437
-chr6	58778788	rs6651013	T	C	3397.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=99;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.86;MQ0=0;QD=34.32;SOR=0.976;VQSLOD=4.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,94:94:99:3426,282,0
-chr6	58778844	rs7452594	C	G	898.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=0.445;ClippingRankSum=-0.341;DB;DP=82;FS=12.217;MLEAC=1;MLEAF=0.5;MQ=58.57;MQ0=0;MQRankSum=0.289;QD=10.96;ReadPosRankSum=1.634;SOR=1.334;VQSLOD=-0.6564;culprit=FS	GT:AD:DP:GQ:PL	0/1:49,29:78:99:927,0,1649
-chr6	58778922	rs6651011	C	A	2529.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.0;AN=2;BaseQRankSum=1.683;ClippingRankSum=1.147;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.77;MQ0=0;MQRankSum=1.586;NEGATIVE_TRAIN_SITE;QD=34.19;ReadPosRankSum=-0.952;SOR=0.246;VQSLOD=-1.389;culprit=FS	GT:AD:DP:GQ:PL	1/1:1,70:71:99:2558,204,0
-chr6	58778989	rs6651015	T	C	2986.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.71;MQ0=0;QD=37.21;SOR=0.722;VQSLOD=4.76;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,69:69:99:3015,208,0
-chr6	58779007	rs6651016	C	T	3187.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.13;MQ0=0;QD=33.52;SOR=0.836;VQSLOD=5.6;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,73:73:99:3216,223,0
-chr6	58779056	rs6937914	T	C	824.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.434;ClippingRankSum=0.011;DB;DP=75;FS=0.903;MLEAC=1;MLEAF=0.5;MQ=59.19;MQ0=0;MQRankSum=-1.194;QD=11.0;ReadPosRankSum=0.535;SOR=0.535;VQSLOD=0.407;culprit=FS	GT:AD:DP:GQ:PL	0/1:41,31:72:99:853,0,1368
-chr6	58779089	rs4286808	C	A	635.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.994;ClippingRankSum=-1.111;DB;DP=63;FS=14.811;MLEAC=1;MLEAF=0.5;MQ=58.97;MQ0=0;MQRankSum=-0.125;NEGATIVE_TRAIN_SITE;QD=10.09;ReadPosRankSum=0.169;SOR=1.477;VQSLOD=-1.459;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,22:62:99:664,0,1572
-chr6	58779097	rs9500231	A	G	1804.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.594;ClippingRankSum=1.075;DB;DP=68;FS=2.521;MLEAC=1;MLEAF=0.5;MQ=58.76;MQ0=0;MQRankSum=-0.173;QD=26.54;ReadPosRankSum=0.414;SOR=0.501;VQSLOD=-0.2854;culprit=DP	GT:AD:DP:GQ:PL	0/1:15,52:67:99:1833,0,403
-chr6	58779308	rs6651018	T	C	16.86	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.004;ClippingRankSum=-0.972;DB;DP=51;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.75;MQ0=0;MQRankSum=-0.526;QD=0.33;ReadPosRankSum=0.43;SOR=0.783	GT:AD:DP:GQ:PL	0/1:42,6:48:45:45,0,1235
-chr6	58779328	rs6651019	A	G	1227.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.0;AN=2;BaseQRankSum=0.974;ClippingRankSum=-1.31;DB;DP=39;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=43.52;MQ0=0;MQRankSum=0.772;QD=31.48;ReadPosRankSum=1.511;SOR=1.675;VQSLOD=0.201;culprit=FS	GT:AD:DP:GQ:PL	1/1:2,35:37:38:1256,38,0
-chr6	58779346	rs4376372	T	G	350.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.662;ClippingRankSum=-0.5;DB;DP=32;FS=2.071;MLEAC=1;MLEAF=0.5;MQ=39.86;MQ0=0;MQRankSum=0.46;QD=10.96;ReadPosRankSum=-0.5;SOR=1.292;VQSLOD=1.45;culprit=QD	GT:AD:DP:GQ:PL	0/1:18,13:31:99:379,0,605
-chr6	58779375	rs4250419	A	G	273.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.795;ClippingRankSum=-0.971;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=30.82;MQ0=0;MQRankSum=-0.442;QD=15.21;ReadPosRankSum=-1.589;SOR=1.781;VQSLOD=3.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,9:18:99:302,0,370
-chr6	58779376	rs6651020	C	T	736.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=17;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=30.93;MQ0=0;QD=27.25;SOR=4.294;VQSLOD=5.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,17:17:54:765,54,0
-chr6	58779409	rs4400241	T	C	160.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.793;ClippingRankSum=1.461;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=32.29;MQ0=0;MQRankSum=0.529;QD=13.4;ReadPosRankSum=1.788;SOR=1.371;VQSLOD=4.57;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,5:12:99:189,0,263
-chr6	58779468	rs6651021	A	G	83.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=30.9;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=4.64;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:28:112,0,28
-chr6	58779499	rs6651022	T	C	49.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=29.0;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.09;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:54:78,0,54
-chr6	61892431	rs4467815	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61909056	rs189688252	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61924395	rs74442497	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61924424	rs149028611	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61939361	rs76899121	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61967504	rs704487	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61967842	rs79961499	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61984979	.	G	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	62017935	rs1997843	T	C	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.5;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	62024599	rs1414786	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62027240	rs1074429	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62034435	rs115639864	C	T	36.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=0.406;QD=6.13;ReadPosRankSum=-0.406;SOR=0.693;VQSLOD=4.21;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,3:6:65:65,0,104
-chr6	62084214	rs3908837	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62114785	rs7742522	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62183331	rs2092608	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62183845	rs35300708	C	CT	19.75	LowQual	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.58;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:56,6,0
-chr6	62198757	rs6916640	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62208255	rs116736672	G	A	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	62217827	rs415716	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62220171	rs387256	A	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	62233173	rs214151	G	C	71.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=41.3;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.02;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	62236450	rs116060945	A	T	18.8	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=9.4;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:46,6,0
-chr6	62252108	rs4598053	C	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.68;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	62252188	rs67145854	GA	G	75.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.13;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	62269382	rs59519746	T	C	18.59	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	62269405	rs56095991	G	T	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	62290945	rs140805963	G	A	44.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.79;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:1,2:3:31:73,0,31
-chr6	62294589	rs115452241	T	C	55.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.43;SOR=1.179;VQSLOD=6.13;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,3:3:9:83,9,0
-chr6	62316285	rs213776	A	C	47.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.88;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:2,2:4:67:76,0,67
-chr6	62329027	rs201975337	A	AT	15.82	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=7.91;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
-chr6	62390916	rs1204114	T	C	2091.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=56;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.71;SOR=0.765;VQSLOD=6.9;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,56:56:99:2120,168,0
-chr6	62413546	rs1204139	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62495041	rs78507898	T	A	20.78	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	62510310	rs1743448	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62515335	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62532253	rs571607	G	C	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.11;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	62582748	.	G	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	62604848	.	T	TTC	69.25	PASS	AC=2;AF=1.0;AN=2;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.21;MQ0=0;QD=13.85;SOR=2.303;VQSLOD=5.37;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:9:106,9,0
-chr6	62650334	rs1114027	T	A	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.08;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	62674103	rs1192455	C	T	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.36;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	62674110	rs1192454	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.92;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	62686434	rs1192430	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62690574	rs1393669	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62706684	rs2102790	C	T	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=7.03;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	62708691	rs9453889	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62757987	rs9346001	C	T	744.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.533;ClippingRankSum=0.028;DB;DP=52;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.661;POSITIVE_TRAIN_SITE;QD=14.32;ReadPosRankSum=1.294;SOR=0.546;VQSLOD=5.4;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:28,24:52:99:773,0,900
-chr6	62886921	rs10455666	C	T	184.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.067;ClippingRankSum=-0.572;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=23.1;ReadPosRankSum=-0.572;SOR=1.863;VQSLOD=6.13;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:2,6:8:59:213,0,59
-chr6	62887031	rs9346218	C	T	1086.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.596;ClippingRankSum=1.848;DB;DP=62;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.846;POSITIVE_TRAIN_SITE;QD=17.53;ReadPosRankSum=-0.056;SOR=0.846;VQSLOD=5.07;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:29,33:62:99:1115,0,921
-chr6	62887099	rs6921170	C	T	1783.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.393;ClippingRankSum=0.055;DB;DP=121;FS=0.706;MLEAC=1;MLEAF=0.5;MQ=59.85;MQ0=0;MQRankSum=0.039;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-0.465;SOR=0.841;VQSLOD=2.95;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:60,60:120:99:1812,0,2047
-chr6	62995920	rs16883133	T	G	157.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-0.572;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=19.72;ReadPosRankSum=1.067;SOR=0.693;VQSLOD=6.06;culprit=FS;GENE=KHDRBS2	GT:AD:DP:GQ:PL	0/1:2,6:8:55:186,0,55
-chr6	63018890	rs9354897	A	G	47.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.76;SOR=1.179;VQSLOD=7.6;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:75,9,0
-chr6	63022153	rs523967	G	A	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=9.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63022286	rs62414811	G	A	58.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	63046505	rs508263	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.8;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63104500	rs2814661	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63116886	rs2452472	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63123748	rs2814696	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63139149	rs2452463	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63167529	rs2881136	G	A	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63171060	rs17381471	C	T	645.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.586;ClippingRankSum=-0.249;DB;DP=71;FS=9.277;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.188;POSITIVE_TRAIN_SITE;QD=9.1;ReadPosRankSum=-0.067;SOR=2.159;VQSLOD=0.69;culprit=QD;GENE=DHFRP5	GT:AD:DP:GQ:PL	0/1:47,24:71:99:674,0,1531
-chr6	63171544	rs648165	A	T	113.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=-0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.38;POSITIVE_TRAIN_SITE;QD=18.96;ReadPosRankSum=1.38;SOR=1.329;VQSLOD=6.18;culprit=FS;GENE=DHFRP5	GT:AD:DP:GQ:PL	0/1:2,4:6:62:142,0,62
-chr6	63251196	rs2345983	C	T	109.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.937;ClippingRankSum=-0.55;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.55;SOR=0.941;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:90:138,0,90
-chr6	63257354	rs9446610	C	T	1142.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.489;ClippingRankSum=-0.017;DB;DP=75;FS=1.132;MLEAC=1;MLEAF=0.5;MQ=58.43;MQ0=0;MQRankSum=-0.447;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=0.337;SOR=0.935;VQSLOD=3.19;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,35:73:99:1171,0,1224
-chr6	63257971	rs6913632	T	C	1383.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.999;ClippingRankSum=0.127;DB;DP=63;FS=2.484;MLEAC=1;MLEAF=0.5;MQ=59.21;MQ0=0;MQRankSum=1.565;POSITIVE_TRAIN_SITE;QD=21.96;ReadPosRankSum=-0.367;SOR=0.382;VQSLOD=1.73;culprit=QD	GT:AD:DP:GQ:PL	0/1:19,44:63:99:1412,0,451
-chr6	63258233	rs11447029	C	CA	15.85	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.718;ClippingRankSum=-1.371;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-0.065;QD=0.99;ReadPosRankSum=0.588;SOR=0.16	GT:AD:DP:GQ:PL	0/1:11,4:15:53:53,0,220
-chr6	63290332	rs9351926	C	A	41.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:70,0,36
-chr6	63309881	rs73762312	G	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	63356605	rs4710365	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63357734	rs66885289	CTT	C	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	63370591	rs7776261	C	A	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	63370651	rs7761764	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63394799	rs4131720	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63426649	rs2752973	C	T	43.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.74;culprit=DP	GT:AD:DP:GQ:PL	0/1:1,2:3:32:72,0,32
-chr6	63480621	rs6937512	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63508240	rs4710370	A	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.3;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63508253	rs4710371	T	A	14.68	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.68;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	63520794	rs7746171	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63522176	rs9352169	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63567509	rs11961562	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63576005	rs55851245	C	G	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	63584587	rs12207161	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	63584592	rs12208504	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	63596076	rs7747071	G	A	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	63596112	rs4307155	C	T	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.9;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63607258	rs10943283	C	A	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63727757	rs9343533	C	A	287.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.833;VQSLOD=6.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:316,24,0
-chr6	63730222	rs9352418	G	T	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	63730266	rs9343536	T	C	47.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	63733880	rs10943404	G	T	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63749658	rs6936280	A	G	59.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	63749860	rs6941288	T	C	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.87;SOR=0.693;VQSLOD=4.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	63753907	rs12208886	A	G	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.6;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	63757242	.	G	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63775888	rs789964	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63785384	rs789954	G	A	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.8;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	63792401	rs1086295	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63863011	rs57238578	G	GGTTGTT	44.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	63874309	rs9343765	G	A	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	63874499	rs7747081	C	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	63885713	rs3059784	T	TTG	26.71	LowQual	AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.71;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:6:63,6,0
-chr6	63885782	rs1020805	T	G	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63902995	rs1847501	G	T	1552.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=6.223;ClippingRankSum=0.5;DB;DP=79;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.817;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.005;SOR=0.743;VQSLOD=4.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,45:79:99:1581,0,943
-chr6	63903354	rs16893840	G	T	550.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.19;ClippingRankSum=0.804;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.89;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=14.49;ReadPosRankSum=0.57;SOR=0.754;VQSLOD=5.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:20,18:38:99:579,0,671
-chr6	63903377	rs6914331	G	A	1128.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=28;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.22;SOR=1.609;VQSLOD=5.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,28:28:84:1157,84,0
-chr6	63903384	rs2047899	G	T	382.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.034;ClippingRankSum=-0.528;DB;DP=28;FS=1.69;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.08;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.345;SOR=0.269;VQSLOD=2.91;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:14,14:28:99:411,0,430
-chr6	63903574	rs142293404	GAAGGAGC	G	121.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=8;FS=3.68;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.754;QD=15.22;ReadPosRankSum=0.0;SOR=2.494;VQSLOD=0.824;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:3,4:7:99:159,0,331
-chr6	63903606	rs116456502	G	A	133.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.72;ClippingRankSum=0.0;DB;DP=6;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-1.38;POSITIVE_TRAIN_SITE;QD=22.29;ReadPosRankSum=1.231;SOR=3.258;VQSLOD=1.17;culprit=DP	GT:AD:DP:GQ:PL	0/1:2,4:6:99:162,0,243
-chr6	63921361	rs4710420	A	G	237.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.72;SOR=4.407;VQSLOD=7.22;culprit=FS;GENE=FKBP1C	GT:AD:DP:GQ:PL	1/1:0,8:8:24:266,24,0
-chr6	63921442	rs76273486	G	A	318.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.127;ClippingRankSum=-0.433;DB;DP=17;FS=3.274;MLEAC=1;MLEAF=0.5;MQ=51.85;MQ0=0;MQRankSum=2.261;POSITIVE_TRAIN_SITE;QD=18.75;ReadPosRankSum=1.299;SOR=1.981;VQSLOD=1.5;culprit=MQRankSum;GENE=FKBP1C	GT:AD:DP:GQ:PL	0/1:8,9:17:99:347,0,251
-chr6	63921456	rs79100944	G	A	493.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.628;ClippingRankSum=-0.102;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.18;MQ0=0;MQRankSum=1.74;QD=22.44;ReadPosRankSum=1.604;SOR=1.402;VQSLOD=0.39;culprit=FS;GENE=FKBP1C	GT:AD:DP:GQ:PL	0/1:8,14:22:99:522,0,233
-chr6	63921924	rs9359357	A	G	278.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.409;ClippingRankSum=-1.184;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.85;MQ0=0;MQRankSum=-1.347;QD=14.67;ReadPosRankSum=1.266;SOR=1.609;VQSLOD=3.62;culprit=FS;GENE=FKBP1C	GT:AD:DP:GQ:PL	0/1:10,9:19:99:307,0,291
-chr6	63933615	rs9352684	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63937797	rs12526013	T	C	105.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.116;ClippingRankSum=-0.735;DB;DP=23;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.41;MQ0=0;MQRankSum=-0.385;POSITIVE_TRAIN_SITE;QD=4.6;ReadPosRankSum=0.175;SOR=0.141;VQSLOD=3.69;culprit=QD;GENE=SPTLC1P3	GT:AD:DP:GQ:PL	0/1:17,6:23:99:134,0,553
-chr6	63937863	rs3925806	T	C	119.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=0.72;POSITIVE_TRAIN_SITE;QD=19.96;ReadPosRankSum=0.72;SOR=0.368;VQSLOD=6.05;culprit=FS;GENE=SPTLC1P3	GT:AD:DP:GQ:PL	0/1:2,4:6:60:148,0,60
-chr6	63937916	rs3925805	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SPTLC1P3	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63939795	rs1809272	T	C	2647.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.907;ClippingRankSum=0.336;DB;DP=202;FS=8.305;MLEAC=1;MLEAF=0.5;MQ=53.46;MQ0=0;MQRankSum=-3.258;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.11;ReadPosRankSum=-0.632;SOR=0.35;VQSLOD=-0.4749;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:107,93:200:99:2676,0,3595
-chr6	63939829	rs1809271	A	T	8543.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=238;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.9;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=0.925;VQSLOD=3.77;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,237:237:99:8572,713,0
-chr6	63940061	rs4035417	A	G	1171.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=2.262;ClippingRankSum=-0.144;DB;DP=64;FS=5.367;MLEAC=1;MLEAF=0.5;MQ=51.76;MQ0=0;MQRankSum=-3.916;NEGATIVE_TRAIN_SITE;QD=18.31;ReadPosRankSum=1.606;SOR=0.207;VQSLOD=-1.9;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:26,38:64:99:1200,0,790
-chr6	63940313	rs6905048	A	C	40.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	63969766	rs9352729	A	G	60.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	63990648	rs35296992	A	G	956.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.261;ClippingRankSum=-0.057;DB;DP=88;FS=2.946;MLEAC=1;MLEAF=0.5;MQ=59.79;MQ0=0;MQRankSum=-0.678;POSITIVE_TRAIN_SITE;QD=10.87;ReadPosRankSum=-0.582;SOR=0.521;VQSLOD=1.69;culprit=QD;GENE=LGSN	GT:AD:DP:GQ:PL	0/1:54,33:87:99:985,0,1782
-chr6	64126837	rs149978231	T	TAC	29.71	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=14.85;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:66,6,0
-chr6	64147016	rs144385019	AAGAAAGGGAGAAGGAAAAGAAAGAAAGG	A	85.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=39.12;MQ0=0;MQRankSum=-0.727;QD=21.43;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.01;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:99:123,0,203
-chr6	64150689	rs10755410	G	A	62.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.404;ClippingRankSum=-0.74;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.185;POSITIVE_TRAIN_SITE;QD=4.83;ReadPosRankSum=1.849;SOR=0.582;VQSLOD=4.9;culprit=QD	GT:AD:DP:GQ:PL	0/1:9,3:12:91:91,0,260
-chr6	64151093	rs9361767	A	G	149.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.572;ClippingRankSum=1.067;DB;DP=8;FS=3.332;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=18.72;ReadPosRankSum=-1.589;SOR=0.105;VQSLOD=1.98;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:2,6:8:54:178,0,54
-chr6	64151771	rs9294215	C	G	107.78	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.731;ClippingRankSum=0.731;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=21.56;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,4:5:25:136,0,25
-chr6	64153691	rs2076874	G	A	46.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	64189643	rs58741217	T	TCAAA	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.13;culprit=FS;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	64190067	rs9443931	C	A	393.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.203;ClippingRankSum=-0.958;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.575;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-1.068;SOR=0.795;VQSLOD=5.07;culprit=FS;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	0/1:11,14:25:99:422,0,388
-chr6	64190278	rs2622276	A	T	386.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.855;ClippingRankSum=-0.153;DB;DP=29;FS=1.455;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.065;POSITIVE_TRAIN_SITE;QD=13.34;ReadPosRankSum=-1.637;SOR=1.112;VQSLOD=2.78;culprit=ReadPosRankSum;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	0/1:14,15:29:99:415,0,464
-chr6	64190446	rs4299811	C	T	145.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.684;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.322;POSITIVE_TRAIN_SITE;QD=18.22;ReadPosRankSum=0.956;SOR=0.33;VQSLOD=6.88;culprit=FS;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	0/1:3,5:8:87:174,0,87
-chr6	64190547	rs4557499	G	T	91.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=8.49;culprit=FS;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	64191578	rs10943822	A	T	30.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.001;ClippingRankSum=0.248;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.248;POSITIVE_TRAIN_SITE;QD=3.42;ReadPosRankSum=0.248;SOR=0.223;VQSLOD=4.86;culprit=QD;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	0/1:6,3:9:59:59,0,364
-chr6	64191586	rs10943823	T	C	73.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.566;ClippingRankSum=-0.382;DB;DP=11;FS=3.09;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.566;POSITIVE_TRAIN_SITE;QD=6.71;ReadPosRankSum=0.715;SOR=0.132;VQSLOD=1.93;culprit=QD;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	0/1:8,3:11:99:102,0,417
-chr6	64191949	rs2800052	C	T	95.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=2.833;VQSLOD=7.66;culprit=FS;GENE=EEF1B2P5	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	64209875	rs1744139	G	A	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	64209877	rs1779772	T	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.4;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	64221239	rs1744145	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64239405	rs1681942	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTP4A1	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64258654	rs1744153	C	T	990.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-3.025;ClippingRankSum=1.004;DB;DP=65;FS=1.109;MLEAC=1;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=0.846;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=1.161;SOR=0.907;VQSLOD=3.16;culprit=FS;GENE=RPL7AP34,PTP4A1	GT:AD:DP:GQ:PL	0/1:32,33:65:99:1019,0,1066
-chr6	64289938	.	AT	A	167.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.598;ClippingRankSum=0.045;DP=221;FS=3.21;MLEAC=1;MLEAF=0.5;MQ=56.34;MQ0=0;MQRankSum=0.356;QD=0.76;ReadPosRankSum=-0.923;SOR=0.391;VQSLOD=0.248;culprit=DP;GENE=PTP4A1	GT:AD:DP:GQ:PL	0/1:132,35:167:99:205,0,2502
-chr6	64322622	rs34430878	CT	C	638.73	PASS	AC=2;AF=1.0;AN=2;BaseQRankSum=1.494;ClippingRankSum=-0.777;DB;DP=34;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.64;MQ0=0;MQRankSum=1.255;QD=18.79;ReadPosRankSum=1.614;SOR=5.353;VQSLOD=3.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:1,28:29:60:676,60,0
-chr6	64322943	rs4583965	C	T	56.84	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=0.727;QD=4.74;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=3.3;culprit=QD	GT:AD:DP:GQ:PL	0/1:1,3:4:18:85,0,18
-chr6	64401952	rs200237690	CATT	C	919.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.674;ClippingRankSum=-0.006;DB;DP=77;FS=1.337;MLEAC=1;MLEAF=0.5;MQ=58.29;MQ0=0;MQRankSum=-2.87;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-0.436;SOR=1.105;VQSLOD=1.29;culprit=MQRankSum;GENE=PHF3	GT:AD:DP:GQ:PL	0/1:45,26:71:99:957,0,2148
-chr6	64419024	.	CT	C	25.74	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.086;ClippingRankSum=-2.457;DP=199;FS=4.601;MLEAC=1;MLEAF=0.5;MQ=57.02;MQ0=0;MQRankSum=0.154;QD=0.13;ReadPosRankSum=-0.94;SOR=0.158;GENE=PHF3	GT:AD:DP:GQ:PL	0/1:142,25:167:63:63,0,2866
-chr6	64472270	rs4710257	A	C	1520.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.301;ClippingRankSum=-0.541;DB;DP=75;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.155;POSITIVE_TRAIN_SITE;QD=20.28;ReadPosRankSum=-1.387;SOR=0.569;VQSLOD=4.26;culprit=FS;GENE=EYS,PHF3	GT:AD:DP:GQ:PL	0/1:32,43:75:99:1549,0,1031
-chr6	64498933	rs147210136	G	A	2218.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.18;ClippingRankSum=0.271;DB;DP=150;FS=9.259;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.467;POSITIVE_TRAIN_SITE;QD=14.79;ReadPosRankSum=1.95;SOR=0.286;VQSLOD=0.949;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:75,74:149:99:2247,0,2088
-chr6	64513363	.	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64523255	.	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64574392	rs10638627	C	CTT	140.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.729;ClippingRankSum=0.729;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.98;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=-0.361;SOR=0.892;VQSLOD=6.6;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:178,0,138
-chr6	64574396	rs10645485	T	TTC	100.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-0.361;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.361;QD=11.19;ReadPosRankSum=-0.361;SOR=0.527;VQSLOD=4.79;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:5,4:9:99:138,0,178
-chr6	64577850	rs321500	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64627882	rs677250	T	C	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.65;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	64686503	rs9362331	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64694354	rs4710457	C	T	3197.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.855;ClippingRankSum=1.756;DB;DP=194;FS=1.841;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.786;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=2.117;SOR=0.546;VQSLOD=2.3;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:92,101:193:99:3226,0,2888
-chr6	64694560	rs1482457	G	A	2447.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.451;ClippingRankSum=0.305;DB;DP=164;FS=1.687;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.165;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=-0.002;SOR=0.497;VQSLOD=2.46;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:89,74:163:99:2476,0,2876
-chr6	64694620	rs1482456	T	C	1132.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.667;ClippingRankSum=0.22;DB;DP=67;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.663;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.755;SOR=1.516;VQSLOD=4.16;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1161,0,1169
-chr6	64708907	rs66502009	A	C	2569.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=3.193;ClippingRankSum=2.479;DB;DP=165;FS=4.658;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.156;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=1.406;SOR=1.162;VQSLOD=1.6;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:81,84:165:99:2598,0,2412
-chr6	64752796	rs10944301	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64840987	rs3013170	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	64885636	rs4310034	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64949401	rs35507550	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64966049	rs2057165	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64968295	rs2057160	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64995013	rs6917553	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65012918	rs9444712	T	C	558.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-4.612;ClippingRankSum=0.176;DB;DP=44;FS=1.724;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.129;POSITIVE_TRAIN_SITE;QD=12.7;ReadPosRankSum=-1.045;SOR=0.412;VQSLOD=2.58;culprit=ReadPosRankSum;GENE=EYS	GT:AD:DP:GQ:PL	0/1:22,22:44:99:587,0,721
-chr6	65013122	rs11753319	C	G	92.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.368;ClippingRankSum=0.421;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=11.6;ReadPosRankSum=0.0;SOR=1.609;VQSLOD=6.06;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:121,0,142
-chr6	65013202	rs7739082	A	C	19.81	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=0.615;ClippingRankSum=-0.168;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.01;MQ0=0;MQRankSum=-0.168;QD=1.04;ReadPosRankSum=0.056;SOR=0.495;GENE=EYS	GT:AD:DP:GQ:PL	0/1:16,3:19:48:48,0,530
-chr6	65021076	rs1922968	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65031098	rs1922975	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65037680	rs614395	G	C	38.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.956;ClippingRankSum=0.322;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=4.85;ReadPosRankSum=-0.322;SOR=0.818;VQSLOD=4.08;culprit=QD;GENE=EYS	GT:AD:DP:GQ:PL	0/1:5,3:8:67:67,0,135
-chr6	65051097	.	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65073876	rs671938	G	T	51.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.53;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	65076921	.	A	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65084617	rs4518475	C	T	44.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=5.99;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:73,0,32
-chr6	65168481	rs35441646	C	CT	30.71	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.35;SOR=0.693;VQSLOD=8.24;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-chr6	65204065	rs13211837	C	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65210797	rs34848022	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65218097	rs9362916	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65229459	rs13202092	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65236845	rs4710276	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65245271	.	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65274426	rs140935331	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65302877	rs75420781	A	T	134.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.58;MQ0=0;MQRankSum=0.198;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=-1.495;SOR=1.609;VQSLOD=5.71;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:2,5:7:61:163,0,61
-chr6	65302898	rs16895524	A	G	263.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.313;ClippingRankSum=1.381;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.97;MQ0=0;MQRankSum=0.533;POSITIVE_TRAIN_SITE;QD=20.29;ReadPosRankSum=0.817;SOR=1.179;VQSLOD=6.63;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:5,8:13:99:292,0,150
-chr6	65302915	rs11331907	GA	G	124.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.088;ClippingRankSum=0.971;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.86;MQ0=0;MQRankSum=-1.678;POSITIVE_TRAIN_SITE;QD=6.93;ReadPosRankSum=2.208;SOR=0.693;VQSLOD=3.97;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:9,9:18:99:162,0,204
-chr6	65302987	rs139235690	ATATCT	A	997.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.5;AN=2;BaseQRankSum=2.195;ClippingRankSum=0.287;DB;DP=46;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.75;MQ0=0;MQRankSum=-3.55;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=3.163;SOR=0.571;VQSLOD=-0.0926;culprit=ReadPosRankSum;GENE=EYS	GT:AD:DP:GQ:PL	0/1:19,26:45:99:1035,0,709
-chr6	65303044	rs199667034	T	G	104.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.183;ClippingRankSum=1.517;DB;DP=59;FS=83.06;MLEAC=1;MLEAF=0.5;MQ=52.39;MQ0=0;MQRankSum=0.3;QD=1.78;ReadPosRankSum=-1.257;SOR=5.992;VQSLOD=-11.36;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:40,19:59:99:133,0,1230
-chr6	65303100	rs17404123	T	C	1344.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.901;ClippingRankSum=-0.677;DB;DP=82;FS=0.838;MLEAC=1;MLEAF=0.5;MQ=54.84;MQ0=0;MQRankSum=-1.556;POSITIVE_TRAIN_SITE;QD=16.4;ReadPosRankSum=0.481;SOR=0.826;VQSLOD=2.46;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:36,46:82:99:1373,0,1059
-chr6	65303381	rs17290119	T	C	46.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.6;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:1,2:3:31:75,0,31
-chr6	65305972	rs11759796	G	A	55.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.24;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	65318362	rs9445030	C	T	61.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.59;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	65341959	rs3028242	T	TATAAC	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.22;culprit=FS;GENE=EYS,HNRNPDP2	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	65365989	rs9445092	T	C	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.17;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	65369802	rs148392797	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65379468	rs1338822	A	T	12.05	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=EYS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:40,0,32
-chr6	65423976	rs9452511	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65430160	rs9354068	C	T	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=5.09;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	65447951	rs70999169	A	AG	84.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.179;VQSLOD=8.62;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	65473673	rs60268597	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65510460	rs34778588	CT	C	514.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.895;ClippingRankSum=-0.724;DB;DP=67;FS=1.771;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=-0.443;QD=7.68;ReadPosRankSum=1.52;SOR=1.167;VQSLOD=0.651;culprit=ReadPosRankSum;GENE=EYS	GT:AD:DP:GQ:PL	0/1:28,30:58:99:552,0,543
-chr6	65523111	rs9345532	A	C	67.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.322;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.92;POSITIVE_TRAIN_SITE;QD=8.47;ReadPosRankSum=-0.322;SOR=0.368;VQSLOD=5.25;culprit=QD;GENE=EYS	GT:AD:DP:GQ:PL	0/1:5,3:8:96:96,0,177
-chr6	65525121	rs1390272	C	T	133.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.271;ClippingRankSum=0.922;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=8.36;ReadPosRankSum=-1.139;SOR=0.412;VQSLOD=5.72;culprit=QD;GENE=EYS	GT:AD:DP:GQ:PL	0/1:10,6:16:99:162,0,313
-chr6	65533004	rs34714059	A	G	223.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.546;ClippingRankSum=-0.296;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.546;POSITIVE_TRAIN_SITE;QD=22.38;ReadPosRankSum=-0.296;SOR=1.609;VQSLOD=5.97;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:3,7:10:91:252,0,91
-chr6	65545787	rs2172886	A	G	63.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.94;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	65553444	rs2643788	A	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65569554	rs2146756	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65596759	rs7743515	G	A	2710.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=75;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.59;SOR=2.895;VQSLOD=5.93;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2739,226,0
-chr6	65611391	rs4710510	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65611814	rs57706332	T	C	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.9;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	65611832	rs142709378	A	C	128.03	PASS	AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=6.74;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-chr6	65611952	rs59518422	T	TATTA	1930.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=44;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=50.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=3.767;VQSLOD=5.99;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1968,132,0
-chr6	65612302	rs75634595	A	G	3301.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.382;ClippingRankSum=-0.22;DB;DP=215;FS=1.153;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=0.451;POSITIVE_TRAIN_SITE;QD=15.36;ReadPosRankSum=2.299;SOR=0.598;VQSLOD=1.86;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:108,107:215:99:3330,0,3121
-chr6	65622463	rs9294631	A	G	2159.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=4.924;ClippingRankSum=-0.947;DB;DP=134;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=1.365;POSITIVE_TRAIN_SITE;QD=16.12;ReadPosRankSum=2.546;SOR=0.693;VQSLOD=3.14;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:70,64:134:99:2188,0,2257
-chr6	65622662	rs9445437	G	C	2121.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=5.294;ClippingRankSum=0.507;DB;DP=143;FS=5.248;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=-0.124;POSITIVE_TRAIN_SITE;QD=14.84;ReadPosRankSum=1.501;SOR=1.441;VQSLOD=1.8;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:81,62:143:99:2150,0,2628
-chr6	65622769	rs74484316	A	G	456.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.723;ClippingRankSum=-1.231;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.336;POSITIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.007;SOR=1.508;VQSLOD=5.31;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:485,0,229
-chr6	65622836	rs41516844	C	A	40.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=6.04;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:2,2:4:69:69,0,76
-chr6	65632558	rs6455016	T	C	256.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=4.174;VQSLOD=6.56;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:285,21,0
-chr6	65678272	rs137904067	C	T	28.77	LowQual	AC=1;AF=0.5;AN=2;BaseQRankSum=-0.922;ClippingRankSum=-0.922;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.922;QD=4.11;ReadPosRankSum=0.922;SOR=0.223;GENE=EYS	GT:AD:DP:GQ:PL	0/1:5,2:7:57:57,0,186
-chr6	65715710	.	G	A	111.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-1.159;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.47;MQ0=0;MQRankSum=-0.876;QD=12.42;ReadPosRankSum=-0.361;SOR=0.368;VQSLOD=4.52;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:140,0,137
-chr6	65721195	rs7751922	G	A	84.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.33;MQ0=0;QD=28.09;SOR=2.833;VQSLOD=7.19;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	65831684	rs9363336	G	A	64.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.84;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	65995024	rs13214404	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65999709	rs6455035	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66005609	rs34666704	AT	A	487.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=20;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.39;SOR=6.091;VQSLOD=6.41;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,20:20:60:525,60,0
-chr6	66005740	rs35045551	G	GA	1585.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.677;ClippingRankSum=-0.71;DB;DP=159;FS=1.564;MLEAC=1;MLEAF=0.5;MQ=59.12;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=9.97;ReadPosRankSum=1.276;SOR=0.921;VQSLOD=1.9;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:79,74:153:99:1623,0,1557
-chr6	66005857	rs17411795	T	A	4088.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.317;ClippingRankSum=-0.64;DB;DP=271;FS=2.014;MLEAC=1;MLEAF=0.5;MQ=59.57;MQ0=0;MQRankSum=1.167;POSITIVE_TRAIN_SITE;QD=15.09;ReadPosRankSum=2.177;SOR=0.759;VQSLOD=1.94;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:136,134:270:99:4117,0,4192
-chr6	66005888	rs9342464	C	T	4205.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=8.627;ClippingRankSum=0.069;DB;DP=251;FS=0.459;MLEAC=1;MLEAF=0.5;MQ=59.72;MQ0=0;MQRankSum=0.018;POSITIVE_TRAIN_SITE;QD=16.76;ReadPosRankSum=0.065;SOR=0.647;VQSLOD=1.79;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:126,125:251:99:4234,0,3830
-chr6	66005970	rs9345601	G	A	3380.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.543;ClippingRankSum=-0.936;DB;DP=213;FS=2.475;MLEAC=1;MLEAF=0.5;MQ=59.91;MQ0=0;MQRankSum=-1.449;POSITIVE_TRAIN_SITE;QD=15.87;ReadPosRankSum=1.107;SOR=0.516;VQSLOD=1.23;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:103,109:212:99:3409,0,3103
-chr6	66006148	rs9342465	A	C	503.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=2.574;ClippingRankSum=0.709;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.485;POSITIVE_TRAIN_SITE;QD=23.99;ReadPosRankSum=0.485;SOR=1.508;VQSLOD=5.36;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:532,0,220
-chr6	66013183	.	G	A	123.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-1.273;ClippingRankSum=-0.27;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=21.81;MQ0=0;MQRankSum=-0.039;QD=6.19;ReadPosRankSum=0.656;SOR=0.368;VQSLOD=3.44;culprit=QD;GENE=EYS	GT:AD:DP:GQ:PL	0/1:12,8:20:99:152,0,259
-chr6	66014572	rs75369872	A	G	25.75	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=22.0;MQ0=0;QD=12.88;SOR=2.303;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:53,6,0
-chr6	66018514	rs117228350	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=46.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66036758	rs13209408	G	A	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.23;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	66045077	rs1502965	C	T	2159.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=61;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.89;SOR=2.584;VQSLOD=6.42;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2188,183,0
-chr6	66045118	rs1502964	T	C	1434.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=42;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.16;SOR=6.091;VQSLOD=6.2;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1463,126,0
-chr6	66053835	rs1502963	T	G	2324.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=56;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.46;SOR=6.666;VQSLOD=7.17;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,56:56:99:2353,168,0
-chr6	66063513	rs1936439	G	A	3064.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-6.245;ClippingRankSum=-0.619;DB;DP=169;FS=3.043;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.296;POSITIVE_TRAIN_SITE;QD=18.13;ReadPosRankSum=1.339;SOR=0.465;VQSLOD=2.08;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:65,104:169:99:3093,0,1991
-chr6	66063766	rs1936440	A	C	48.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.26;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:1,2:3:33:77,0,33
-chr6	66066936	rs9294638	G	T	172.9	PASS	AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.58;SOR=1.981;VQSLOD=6.69;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:201,15,0
-chr6	66067315	rs976727	A	C	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.3;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	66080074	rs9342469	G	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66112409	rs974110	A	G	2596.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-2.384;ClippingRankSum=-0.001;DB;DP=191;FS=0.54;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.531;POSITIVE_TRAIN_SITE;QD=13.6;ReadPosRankSum=3.882;SOR=0.763;VQSLOD=1.48;culprit=ReadPosRankSum;GENE=EYS	GT:AD:DP:GQ:PL	0/1:102,89:191:99:2625,0,3119
-chr6	66115281	rs34154043	G	GAAA	3245.73	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=-5.314;ClippingRankSum=1.32;DB;DP=225;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.08;MQ0=0;MQRankSum=0.881;POSITIVE_TRAIN_SITE;QD=14.43;ReadPosRankSum=-2.39;SOR=0.705;VQSLOD=1.12;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	0/1:99,90:189:99:3283,0,3862
-chr6	66141229	.	T	C	20.78	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	66160560	rs9354246	A	G	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.68;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	66201364	rs9363379	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66204945	rs12193967	G	A	2169.77	PASS	AC=1;AF=0.5;AN=2;BaseQRankSum=1.754;ClippingRankSum=-0.093;DB;DP=128;FS=4.193;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-0.577;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=1.481;SOR=0.652;VQSLOD=2.12;culprit=DP;GENE=EYS	GT:AD:DP:GQ:PL	0/1:58,70:128:99:2198,0,1773
-chr6	66288101	rs150888347	A	AAT	77.25	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.36;MQ0=0;QD=25.75;SOR=1.179;VQSLOD=7.22;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:114,9,0
-chr6	66336763	rs6903740	T	C	42.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.26;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	66336907	rs71736895	CCTTT	C	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.89;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66351345	rs6925080	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66375671	rs7757773	A	T	46.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.43;SOR=1.179;VQSLOD=7.21;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:74,9,0
-chr6	66379893	rs57880191	ACTC	A	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.36;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66379911	rs9283820	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.76;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66394859	rs1490125	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66409784	rs2812776	A	G	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.75;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66409789	rs2814115	T	C	62.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.59;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66411331	rs1490130	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66417384	rs9294647	G	T	52.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.92;culprit=FS;GENE=EYS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	66418352	rs1490129	T	C	233.8	PASS	AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.4;SOR=0.941;VQSLOD=6.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:262,21,0
-chr6	66418415	rs4609011	T	C	54.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	66456318	rs2636129	T	C	49.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	66456442	rs12526256	C	T	92.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=1.179;VQSLOD=8.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:120,9,0
-chr6	66471880	rs9453396	T	G	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66471897	rs9453397	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66471949	rs9445579	C	A	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.8;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	66524243	rs2802047	C	T	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66546565	rs4388276	G	A	48.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.99;culprit=FS;GENE=ADH5P4	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	66547178	rs4392709	G	A	7412.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=208;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.34;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.53;SOR=0.857;VQSLOD=5.34;culprit=QD;GENE=ADH5P4	GT:AD:DP:GQ:PL	1/1:0,208:208:99:7441,625,0
-chr6	66547322	rs9363455	T	G	5109.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=152;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=33.62;SOR=1.319;VQSLOD=4.64;culprit=FS;GENE=ADH5P4	GT:AD:DP:GQ:PL	1/1:0,152:152:99:5138,456,0
-chr6	66568995	rs6931427	G	A	62.28	PASS	AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	66596125	rs9283821	G	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66610269	rs9363483	A	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66710291	rs1484569	C	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66763069	rs1385225	A	G	57.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	66763131	.	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66802808	rs4710310	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66803535	rs2881644	C	A	8655.77	PASS	AC=2;AF=1.0;AN=2;DB;DP=238;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=0.789;VQSLOD=5.13;culprit=FS;GENE=NUFIP1P	GT:AD:DP:GQ:PL	1/1:0,237:237:99:8684,713,0
-chr6	66803769	rs55951409	G	GGTTTCT	2785.73	PASS	AC=2;AF=1.0;AN=2;DB;DP=59;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=31.86;MQ0=0;QD=27.53;SOR=0.96;VQSLOD=4.58;culprit=FS;GENE=NUFIP1P	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2823,189,0
-chr6	66804609	rs147166458	GACTC	G	322.75	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.87;SOR=1.179;VQSLOD=5.97;culprit=FS;GENE=NUFIP1P	GT:AD:DP:GQ:PL	1/1:0,8:8:24:360,24,0
-chr6	66804622	rs3925325	G	C	368.78	PASS	AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.49;MQ0=0;QD=30.3;SOR=1.179;VQSLOD=5.58;culprit=FS;GENE=NUFIP1P	GT:AD:DP:GQ:PL	1/1:0,8:8:27:397,27,0
-chr6	66804958	rs3030466	C	CCT	52.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.35;SOR=2.303;VQSLOD=8.57;culprit=FS;GENE=NUFIP1P	GT:AD:DP:GQ:PL	1/1:0,2:2:6:89,6,0
-chr6	66807446	rs7738469	T	C	53.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	66818604	rs3846808	T	C	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66829961	rs11287287	AG	A	38.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	66836869	rs13217074	A	G	56.74	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	66849936	rs866452	T	A	21.77	LowQual	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66871532	rs138893096	C	CAAAG	53.7	PASS	AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
diff --git a/run.py b/run.py
index d52e909..51236dc 100755
--- a/run.py
+++ b/run.py
@@ -1,46 +1,65 @@
 #!/usr/bin/env python
 import argparse
 import json
-import logging
 import sys
+import os
 
 from variantapi.client import VariantAPIClient
 
 __author__ = 'ckopanos'
-logging.basicConfig(level=logging.DEBUG,
-                    format='[%(levelname)s]	%(threadName)s	%(message)s',
-                    )
 
 
-def main(argv):
+def annotate_variant(argv):
     parser = argparse.ArgumentParser(description='Sample Variant API calls')
     parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
     parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
                         required=False, default='hg19')
     parser.add_argument('-q',
                         help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request '
-                             'e.g. chr19:20082943:1:G rs113488022',
-                        type=str, metavar='Query', required=True, nargs='+')
+                             'e.g. chr19:20082943:1:G rs113488022. Don\'t use it together with the -i option',
+                        type=str, metavar='Query', required=False, nargs='+')
     parser.add_argument('-p',
                         help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
                         type=str, metavar='Request Params', required=False, nargs='+')
+    parser.add_argument('-i',
+                        help='Path to csv file with variants. It should include one variant per line. Don\'t use it '
+                             'together with the -q option',
+                        type=str, metavar='CSV File', required=False)
+    parser.add_argument('-o',
+                        help='Path to output file to store variant annotations',
+                        type=str, metavar='CSV File', required=False)
     args = parser.parse_args()
     api_key = args.k
     query = args.q
     ref_genome = args.g
+    input_file = args.i
+    output_file = args.o
+    if query and input_file:
+        sys.stderr.write("Don't specify -i and -q options together. Use only one of them")
+        sys.exit(1)
+    if not query and not input_file:
+        sys.stderr.write("Please either specify -i or -q options")
+        sys.exit(1)
+    if input_file and not os.path.exists(input_file):
+        sys.stderr.write('File %s does not exist' % input_file)
+        sys.exit(1)
+    if output_file and not os.path.exists(output_file):
+        sys.stderr.write('File %s already exists' % input_file)
+        sys.exit(1)
     request_parameters = None
     if args.p:
         request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
     api = VariantAPIClient(api_key)
+
     if len(query) == 1:
         result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome)
     else:
         if api_key is None:
             sys.exit("You need to pass an api key to perform batch requests")
-        result = api.batch_lookup(query, params=request_parameters,  ref_genome=ref_genome)
+        result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome)
     sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
     sys.stdout.write("\n")
 
 
 if __name__ == "__main__":
-    main(sys.argv[1:])
+    annotate_variant(sys.argv[1:])
diff --git a/sample.vcf b/sample.vcf
deleted file mode 100644
index 94cd3d1..0000000
--- a/sample.vcf
+++ /dev/null
@@ -1,2132 +0,0 @@
-##fileformat=VCFv4.1
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.4085 <= x < 0.0794">
-##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -1678.3953">
-##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1678.3953 <= x < -2.4085">
-##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.501 <= x < 0.319">
-##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -1474.3646">
-##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1474.3646 <= x < -1.501">
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##GATKCommandLine=<ID=ApplyRecalibration,Version=3.3-0-g37228af,Date="Tue Jun 30 08:48:57 CEST 2015",Epoch=1435646937859,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ref/genomes/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=gatk/raw.variants.vcf)] recal_file=(RodBinding name=recal_file source=gatk/recalibrate_SNP.recal) tranches_file=gatk/recalibrate_SNP.tranches out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=ApplyRecalibration,Version=3.3-0-g37228af,Date="Tue Jun 30 08:49:46 CEST 2015",Epoch=1435646986265,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ref/genomes/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=gatk/recalibrated_snps_raw_indels.vcf)] recal_file=(RodBinding name=recal_file source=gatk/recalibrate_INDEL.recal) tranches_file=gatk/recalibrate_INDEL.tranches out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Tue Jun 30 02:53:50 CEST 2015",Epoch=1435625630685,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[bam/recalibrated.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ref/genomes/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name=dbsnp source=/ref/genomes/hg19/broad/dbsnp_138.hg19.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
-##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
-##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
-##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
-##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
-##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
-##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
-##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
-##contig=<ID=chrM,length=16571,assembly=hg19>
-##contig=<ID=chr1,length=249250621,assembly=hg19>
-##contig=<ID=chr2,length=243199373,assembly=hg19>
-##contig=<ID=chr3,length=198022430,assembly=hg19>
-##contig=<ID=chr4,length=191154276,assembly=hg19>
-##contig=<ID=chr5,length=180915260,assembly=hg19>
-##contig=<ID=chr6,length=171115067,assembly=hg19>
-##contig=<ID=chr7,length=159138663,assembly=hg19>
-##contig=<ID=chr8,length=146364022,assembly=hg19>
-##contig=<ID=chr9,length=141213431,assembly=hg19>
-##contig=<ID=chr10,length=135534747,assembly=hg19>
-##contig=<ID=chr11,length=135006516,assembly=hg19>
-##contig=<ID=chr12,length=133851895,assembly=hg19>
-##contig=<ID=chr13,length=115169878,assembly=hg19>
-##contig=<ID=chr14,length=107349540,assembly=hg19>
-##contig=<ID=chr15,length=102531392,assembly=hg19>
-##contig=<ID=chr16,length=90354753,assembly=hg19>
-##contig=<ID=chr17,length=81195210,assembly=hg19>
-##contig=<ID=chr18,length=78077248,assembly=hg19>
-##contig=<ID=chr19,length=59128983,assembly=hg19>
-##contig=<ID=chr20,length=63025520,assembly=hg19>
-##contig=<ID=chr21,length=48129895,assembly=hg19>
-##contig=<ID=chr22,length=51304566,assembly=hg19>
-##contig=<ID=chrX,length=155270560,assembly=hg19>
-##contig=<ID=chrY,length=59373566,assembly=hg19>
-##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
-##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
-##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
-##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
-##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
-##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
-##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
-##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
-##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
-##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
-##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
-##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
-##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
-##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
-##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
-##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
-##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
-##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
-##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
-##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
-##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
-##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
-##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
-##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
-##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
-##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
-##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
-##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
-##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
-##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
-##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
-##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
-##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
-##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
-##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
-##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
-##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
-##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
-##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
-##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
-##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
-##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
-##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
-##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
-##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
-##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
-##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
-##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
-##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
-##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
-##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
-##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
-##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
-##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
-##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
-##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
-##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
-##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
-##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
-##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
-##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
-##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
-##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
-##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
-##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
-##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
-##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
-##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
-##reference=file:///ref/genomes/hg19/hg19.fa
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR309291
-chr6	44387517	rs6923521	C	G	184.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.81;SOR=3.912;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:18:213,18,0
-chr6	44410746	rs61581947	GT	G	17.78	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=5.93;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:54,6,0
-chr6	44453701	rs60176543	G	A	15.65	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	44505655	rs9296442	G	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	44526440	rs991234	A	C	36.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.37;SOR=0.693;VQSLOD=7.54;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:64,6,0
-chr6	44532454	rs76750540	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44547060	rs67452991	C	T	102.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.51;SOR=0.693;VQSLOD=5.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:130,12,0
-chr6	44562107	rs491616	G	C	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:28:40,0,28
-chr6	44575012	rs636287	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44584484	rs634631	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44585311	rs648579	T	C	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.91;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	44586011	rs651831	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44586363	rs6913259	C	T	171.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=6.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:200,15,0
-chr6	44595393	rs1767788	C	T	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=9.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	44605066	rs6934182	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44605461	rs4714809	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44629576	rs4257850	A	G	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	44635852	rs4711794	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44640206	rs527082	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44775098	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44780682	rs622923	G	T	14.68	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.34;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	44780701	rs559322	C	T	15.65	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	44781313	rs5875893	G	GA	15.82	LowQual	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=3.95;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
-chr6	44797271	rs9369514	C	A	241.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.54;SOR=2.584;VQSLOD=6.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:270,21,0
-chr6	44825715	rs9395051	C	A	71.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=7.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	44834094	rs3846896	G	A	15.65	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	44840376	rs1293588	A	C	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	44888740	rs608941	C	T	94.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.87;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	44899632	rs679713	T	C	1144.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.54;SOR=6.666;VQSLOD=6.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,27:27:81:1173,81,0
-chr6	44900253	rs3799986	A	G	188.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.64;SOR=3.611;VQSLOD=6.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:217,15,0
-chr6	44903248	rs10948186	C	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	44921320	rs10948187	C	T	89.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=2.833;VQSLOD=8.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:117,9,0
-chr6	44921962	rs625782	T	C	65.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=2.833;VQSLOD=7.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:93,9,0
-chr6	44935341	rs636845	C	T	60.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=8.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	44952716	rs5875900	GT	G	29.71	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.85;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:66,6,0
-chr6	44972729	rs1159132	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	44988149	rs1475534	C	T	529.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.74;SOR=5.421;VQSLOD=7.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,14:14:42:558,42,0
-chr6	45003928	rs4398713	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45020697	rs2149872	A	G	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	45066168	rs150556986	G	A	167.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.388;ClippingRankSum=0.194;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.194;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=-0.968;SOR=1.402;VQSLOD=5.50;culprit=FS	GT:AD:DP:GQ:PL	0/1:8,6:14:99:196,0,294
-chr6	45073967	rs2396381	A	G	88.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.43;SOR=2.833;VQSLOD=8.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:116,9,0
-chr6	45090876	.	T	C	19.79	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.89;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:47,6,0
-chr6	45159414	rs11321900	TA	T	24.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	45163350	rs1748242	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45170121	rs1284955	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45175908	rs9381373	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45177025	rs2396425	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45192941	rs6911320	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45203918	rs6937317	T	C	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	45268574	rs111541141	T	TAAGAC	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	45360194	rs9395099	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45390962	rs11498196	C	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	45444061	rs2677110	C	T	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=9.10;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	45444083	rs35663521	G	GA	38.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=7.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	45456564	rs12215249	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45486207	rs7771889	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45511541	rs10948238	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45519443	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45521733	rs1201807	C	T	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	45521847	rs70996341	ATGTG	A	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	45523928	rs675613	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45523947	rs5875926	G	GA	24.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	45564510	rs713270	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45609347	.	G	GT	22.73	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=11.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:59,6,0
-chr6	45705659	rs829913	T	A	96.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	45733276	rs6942337	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45749983	rs9357491	A	G	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	45754997	rs1037281	A	C	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=9.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	45764956	rs11276783	ACAGGGCAGCT	A	98.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.75;SOR=2.833;VQSLOD=7.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	45769869	rs10948257	G	A	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=7.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	45792170	rs12197564	G	T	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	45808216	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45833836	rs142466444	TTTTC	T	85.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=17.15;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:43:123,0,43
-chr6	45847678	rs2396559	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45851886	rs1932042	C	T	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	45858548	rs71566550	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45870999	rs35735653	CAG	C	269.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.457;DB;DP=33;FS=4.212;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.588;POSITIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=0.239;SOR=1.802;VQSLOD=2.22;culprit=FS	GT:AD:DP:GQ:PL	0/1:22,9:31:99:307,0,882
-chr6	45888576	rs34155361	ATGC	A	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	45893031	rs6939554	C	T	35.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.87;SOR=0.693;VQSLOD=7.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:63,6,0
-chr6	45901916	rs9349337	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45909139	rs11421773	C	CG	234.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.08;SOR=2.833;VQSLOD=6.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:27:272,27,0
-chr6	45914028	rs3777582	A	T	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.72;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	45915413	rs1890368	C	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	45915504	rs1890369	A	C	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	45919719	rs3777587	A	G	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=6.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	45919758	rs3777588	G	A	120.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=24.16;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,4:5:27:149,0,27
-chr6	45921108	rs3777590	G	C	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	45922849	rs3734206	C	T	1890.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.58;SOR=6.316;VQSLOD=6.34;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1919,141,0
-chr6	45923126	rs6909306	A	C	252.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.60;SOR=4.407;VQSLOD=6.96;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:281,24,0
-chr6	45965608	rs3777612	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45989366	rs1204338	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	45994992	rs1547605	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46025834	rs1535110	T	G	23.58	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=7.86;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:7:51,7,0
-chr6	46047269	rs9381423	T	C	124.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.945;ClippingRankSum=0.453;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-1.586;POSITIVE_TRAIN_SITE;QD=7.80;ReadPosRankSum=1.586;SOR=0.223;VQSLOD=4.04;culprit=QD	GT:AD:DP:GQ:PL	0/1:11,5:16:99:153,0,375
-chr6	46047458	rs3734207	C	T	3075.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.190;ClippingRankSum=-0.231;DB;DP=213;FS=0.542;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-1.583;POSITIVE_TRAIN_SITE;QD=14.44;ReadPosRankSum=0.457;SOR=0.754;VQSLOD=1.68;culprit=FS	GT:AD:DP:GQ:PL	0/1:107,105:212:99:3104,0,3533
-chr6	46048000	rs1416165	T	C	2778.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.171;ClippingRankSum=0.218;DB;DP=172;FS=0.639;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.131;POSITIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=-1.044;SOR=0.794;VQSLOD=1.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:74,98:172:99:2807,0,2169
-chr6	46107115	rs61381984	A	AT	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=4;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=3.01;ReadPosRankSum=0.736;SOR=2.225	GT:AD:DP:GQ:PL	0/1:1,2:3:20:49,0,20
-chr6	46107312	rs11752816	G	A	1890.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.790;ClippingRankSum=0.077;DB;DP=125;FS=3.508;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.580;POSITIVE_TRAIN_SITE;QD=15.13;ReadPosRankSum=-1.351;SOR=0.335;VQSLOD=2.14;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:62,63:125:99:1919,0,1762
-chr6	46107752	rs7451713	C	G	5119.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=7.032;ClippingRankSum=-2.826;DB;DP=301;FS=1.419;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.805;POSITIVE_TRAIN_SITE;QD=17.01;ReadPosRankSum=0.708;SOR=0.792;VQSLOD=1.55;culprit=DP	GT:AD:DP:GQ:PL	0/1:146,155:301:99:5148,0,4240
-chr6	46110821	rs7769902	A	G	202.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.085;ClippingRankSum=0.380;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-0.211;POSITIVE_TRAIN_SITE;QD=10.67;ReadPosRankSum=-0.549;SOR=0.321;VQSLOD=4.71;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,7:19:99:231,0,378
-chr6	46110844	rs35942390	T	TGA	174.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;ClippingRankSum=-0.444;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=1.467;POSITIVE_TRAIN_SITE;QD=6.47;ReadPosRankSum=-0.853;SOR=0.307;VQSLOD=5.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,8:22:99:212,0,429
-chr6	46124799	rs9367237	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46129345	rs2235881	G	A	4707.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.532;ClippingRankSum=-0.307;DB;DP=317;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=0.655;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=2.066;SOR=0.698;VQSLOD=1.89;culprit=FS	GT:AD:DP:GQ:PL	0/1:162,154:316:99:4736,0,4689
-chr6	46135489	rs6926570	T	C	3065.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.245;ClippingRankSum=0.018;DB;DP=187;FS=1.135;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.009;POSITIVE_TRAIN_SITE;QD=16.39;ReadPosRankSum=1.610;SOR=0.809;VQSLOD=2.66;culprit=DP	GT:AD:DP:GQ:PL	0/1:96,91:187:99:3094,0,2997
-chr6	46135984	rs3806995	G	T	1685.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.855;ClippingRankSum=-0.003;DB;DP=117;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=14.41;ReadPosRankSum=2.665;SOR=0.727;VQSLOD=4.05;culprit=FS	GT:AD:DP:GQ:PL	0/1:61,56:117:99:1714,0,1985
-chr6	46148778	rs34512199	AT	A	24.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	46170924	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46206776	rs55832349	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46219283	rs6910477	G	A	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	46259017	rs11389800	G	GT	13.89	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=4.63;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:50,6,0
-chr6	46293328	rs2277121	G	A	717.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=5.994;VQSLOD=6.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,19:19:57:746,57,0
-chr6	46296710	rs6906742	C	T	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	46302975	rs60870663	T	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46302987	rs58585138	A	G	46.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	46312875	rs9367242	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46321514	.	T	C	20.78	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	46326865	.	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46456536	rs9349362	C	T	33.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:34:62,0,34
-chr6	46462514	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46469927	rs59470467	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46470622	rs67200907	G	A	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	46479322	rs1609661	A	G	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	46490097	rs4714943	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46512200	.	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46521602	rs699939	C	A	599.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.640;ClippingRankSum=0.714;DB;DP=46;FS=1.296;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.647;POSITIVE_TRAIN_SITE;QD=13.04;ReadPosRankSum=2.186;SOR=0.911;VQSLOD=2.11;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:27,19:46:99:628,0,724
-chr6	46563817	rs7761731	A	T	3102.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.173;ClippingRankSum=-1.345;DB;DP=194;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=0.519;POSITIVE_TRAIN_SITE;QD=15.99;ReadPosRankSum=0.699;SOR=0.739;VQSLOD=2.35;culprit=FS	GT:AD:DP:GQ:PL	0/1:90,104:194:99:3131,0,2802
-chr6	46607081	rs3085602	AT	A	645.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.29;SOR=6.091;VQSLOD=5.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,20:20:60:683,60,0
-chr6	46620252	rs12192544	C	G	5715.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.691;ClippingRankSum=0.485;DB;DP=440;FS=1.133;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-2.934;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.99;ReadPosRankSum=-0.818;SOR=0.805;VQSLOD=-9.355e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:239,200:439:99:5744,0,6851
-chr6	46623698	rs3757241	T	C	6720.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=183;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.06;SOR=0.822;VQSLOD=5.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,179:179:99:6749,538,0
-chr6	46625274	rs9381468	A	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.35;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	46626353	rs953062	A	G	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	46630068	rs9381469	G	A	907.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.991;ClippingRankSum=-0.318;DB;DP=68;FS=14.136;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.231;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=1.115;SOR=3.003;VQSLOD=1.21;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,28:68:99:936,0,1206
-chr6	46637908	rs200254015	A	C	76.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.158;ClippingRankSum=-1.074;DB;DP=72;FS=148.770;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.756;QD=1.07;ReadPosRankSum=-5.463;SOR=5.781;VQSLOD=-4.745e+01;culprit=FS	GT:AD:DP:GQ:PL	0/1:55,17:72:99:105,0,1883
-chr6	46649231	rs7740677	C	T	6652.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=183;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.56;SOR=2.067;VQSLOD=5.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,183:183:99:6681,550,0
-chr6	46657057	rs3799277	A	G	4300.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=112;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.78;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.29;SOR=1.350;VQSLOD=6.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,111:111:99:4329,334,0
-chr6	46658905	rs9381472	C	G	2370.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.957;ClippingRankSum=-1.243;DB;DP=147;FS=3.996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.165;POSITIVE_TRAIN_SITE;QD=16.13;ReadPosRankSum=0.979;SOR=1.036;VQSLOD=2.15;culprit=DP	GT:AD:DP:GQ:PL	0/1:77,70:147:99:2399,0,2735
-chr6	46661937	rs55724083	CT	C	307.76	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.021;ClippingRankSum=0.615;DB;DP=81;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.11;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=3.80;ReadPosRankSum=0.542;SOR=3.026;VQSLOD=5.76;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,30:36:22:345,0,22
-chr6	46672205	.	TCTCTCTCTCTCA	T	62.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;ClippingRankSum=0.361;DP=48;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.85;MQ0=0;MQRankSum=-1.307;QD=1.31;ReadPosRankSum=2.219;SOR=0.892;VQSLOD=2.56;culprit=FS	GT:AD:DP:GQ:PL	0/1:15,5:20:99:100,0,440
-chr6	46672452	rs148052037	TAATC	T	1973.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.650;ClippingRankSum=1.355;DB;DP=107;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=0;MQRankSum=-2.444;POSITIVE_TRAIN_SITE;QD=18.45;ReadPosRankSum=-0.854;SOR=0.718;VQSLOD=3.96;culprit=FS	GT:AD:DP:GQ:PL	0/1:51,52:103:99:2011,0,3030
-chr6	46672943	rs1051931	A	G	6548.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=172;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.43;SOR=1.172;VQSLOD=3.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,170:170:99:6577,511,0
-chr6	46676019	rs2216465	C	G	430.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.311;ClippingRankSum=0.241;DB;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.548;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=-0.022;SOR=0.518;VQSLOD=5.37;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,13:29:99:459,0,615
-chr6	46682079	rs1362931	A	C	1919.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.23;SOR=7.864;VQSLOD=7.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1948,150,0
-chr6	46683978	rs41361844	T	TA	363.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.549;ClippingRankSum=1.214;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.33;MQ0=0;MQRankSum=-0.419;POSITIVE_TRAIN_SITE;QD=11.02;ReadPosRankSum=1.046;SOR=0.473;VQSLOD=6.00;culprit=FS	GT:AD:DP:GQ:PL	0/1:17,13:30:99:401,0,436
-chr6	46684222	rs1805017	C	T	2595.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.964;ClippingRankSum=-0.355;DB;DP=171;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=1.275;POSITIVE_TRAIN_SITE;QD=15.18;ReadPosRankSum=0.601;SOR=0.648;VQSLOD=2.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:85,85:170:99:2624,0,2396
-chr6	46685286	rs6929105	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46689762	rs9472830	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46695144	.	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46714081	rs141667902	GTTCTCC	G	187.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.03;MQ0=0;QD=31.31;SOR=1.022;VQSLOD=5.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:225,15,0
-chr6	46727772	rs6918050	G	C	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.87;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	46730039	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46761495	rs2274656	G	A	1258.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.705;ClippingRankSum=0.492;DB;DP=66;FS=11.133;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=19.07;ReadPosRankSum=0.794;SOR=0.077;VQSLOD=0.934;culprit=FS	GT:AD:DP:GQ:PL	0/1:26,40:66:99:1287,0,859
-chr6	46766467	rs872018	G	C	826.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.434;ClippingRankSum=0.387;DB;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=0;MQRankSum=0.716;POSITIVE_TRAIN_SITE;QD=18.37;ReadPosRankSum=-3.462;SOR=1.681;VQSLOD=3.22;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:22,22:44:99:855,0,1647
-chr6	46766468	rs872019	G	C	826.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.555;ClippingRankSum=-0.670;DB;DP=46;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-0.329;POSITIVE_TRAIN_SITE;QD=17.97;ReadPosRankSum=-2.986;SOR=1.609;VQSLOD=4.20;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:23,22:45:99:855,0,1647
-chr6	46775361	rs2894714	A	G	95.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.76;SOR=1.179;VQSLOD=6.48;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	46777377	rs1833460	T	C	2742.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.37;SOR=5.892;VQSLOD=6.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,78:78:99:2771,235,0
-chr6	46784183	rs9367257	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	46793175	rs6920863	G	A	976.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.347;ClippingRankSum=0.690;DB;DP=69;FS=2.675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.762;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=-0.654;SOR=0.378;VQSLOD=3.19;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:35,34:69:99:1005,0,1233
-chr6	46794048	rs2297018	C	G	1559.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.778;ClippingRankSum=1.150;DB;DP=86;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.527;POSITIVE_TRAIN_SITE;QD=18.14;ReadPosRankSum=-0.821;SOR=0.791;VQSLOD=4.49;culprit=FS	GT:AD:DP:GQ:PL	0/1:41,45:86:99:1588,0,1376
-chr6	46797329	rs2274657	G	A	1320.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.675;ClippingRankSum=0.827;DB;DP=98;FS=1.251;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=-0.371;POSITIVE_TRAIN_SITE;QD=13.48;ReadPosRankSum=0.307;SOR=0.399;VQSLOD=3.23;culprit=DP	GT:AD:DP:GQ:PL	0/1:53,45:98:99:1349,0,1847
-chr6	46797515	rs6903045	G	A	68.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.406;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,3:6:73:97,0,73
-chr6	46801071	rs2274658	G	T	2458.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.720;ClippingRankSum=0.231;DB;DP=169;FS=2.721;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.436;POSITIVE_TRAIN_SITE;QD=14.55;ReadPosRankSum=2.140;SOR=0.917;VQSLOD=2.52;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:89,80:169:99:2487,0,2786
-chr6	46802172	.	ATATTTATT	A	98.25	PASS	AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	46802370	rs4714952	G	A	4383.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=119;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.22;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.86;SOR=1.198;VQSLOD=7.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,119:119:99:4412,357,0
-chr6	46802901	rs2297021	G	C	87.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=0.720;POSITIVE_TRAIN_SITE;QD=14.63;ReadPosRankSum=-0.720;SOR=0.368;VQSLOD=5.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:67:116,0,67
-chr6	46803018	rs2297020	A	T	292.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;ClippingRankSum=0.040;DB;DP=32;FS=3.467;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=0.913;POSITIVE_TRAIN_SITE;QD=9.15;ReadPosRankSum=-0.357;SOR=1.659;VQSLOD=2.47;culprit=QD	GT:AD:DP:GQ:PL	0/1:21,11:32:99:321,0,590
-chr6	46803102	rs2297019	A	G	273.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.297;ClippingRankSum=-1.681;DB;DP=23;FS=1.740;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-1.484;POSITIVE_TRAIN_SITE;QD=11.90;ReadPosRankSum=-0.495;SOR=0.925;VQSLOD=2.16;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:12,10:22:99:302,0,349
-chr6	46803345	rs12196017	G	A	98.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.550;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.07;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=14.11;ReadPosRankSum=1.754;SOR=0.941;VQSLOD=6.35;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:96:127,0,96
-chr6	46806766	rs115391170	G	A	1395.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.528;ClippingRankSum=0.481;DB;DP=95;FS=14.804;MLEAC=1;MLEAF=0.500;MQ=56.80;MQ0=0;MQRankSum=2.724;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=14.69;ReadPosRankSum=1.677;SOR=0.144;VQSLOD=-1.508e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1424,0,1271
-chr6	46806802	rs143826629	G	A	1031.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.214;ClippingRankSum=0.523;DB;DP=71;FS=2.497;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=0.719;QD=14.53;ReadPosRankSum=-0.144;SOR=0.401;VQSLOD=1.61;culprit=DP	GT:AD:DP:GQ:PL	0/1:36,35:71:99:1060,0,1434
-chr6	46806809	rs1804211	C	T	1130.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.852;ClippingRankSum=0.535;DB;DP=71;FS=1.182;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-0.121;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=1.122;SOR=0.995;VQSLOD=3.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,37:71:99:1159,0,1325
-chr6	46806939	rs17468190	G	T	181.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.380;ClippingRankSum=0.244;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.24;MQ0=0;MQRankSum=-1.977;POSITIVE_TRAIN_SITE;QD=12.98;ReadPosRankSum=0.689;SOR=1.022;VQSLOD=4.95;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,7:12:99:210,0,155
-chr6	46806948	rs150225810	G	GTTTGGGGCAGCT	230.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.62;MQ0=0;QD=19.23;SOR=3.912;VQSLOD=4.37;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:17:268,17,0
-chr6	46807040	rs1059276	C	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46817550	rs6929917	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46817982	rs6458525	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.65;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46821191	.	A	G	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:28:40,0,28
-chr6	46822349	rs475991	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46823695	rs657340	G	A	1861.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.21;SOR=1.893;VQSLOD=6.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1890,156,0
-chr6	46823805	rs58687946	A	AG	1627.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.74;MQ0=0;QD=32.55;SOR=2.511;VQSLOD=4.68;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1665,138,0
-chr6	46824279	rs526123	A	G	176.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.248;ClippingRankSum=1.203;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=0;MQRankSum=-1.683;POSITIVE_TRAIN_SITE;QD=19.64;ReadPosRankSum=-0.573;SOR=1.402;VQSLOD=5.29;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,6:9:92:205,0,92
-chr6	46824448	rs643409	A	G	2848.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.32;SOR=1.816;VQSLOD=7.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,83:83:99:2877,250,0
-chr6	46824798	rs521502	C	G	420.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=4.977;VQSLOD=6.96;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,11:11:33:449,33,0
-chr6	46825595	rs2281443	G	A	37.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=8.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:65,6,0
-chr6	46825632	rs627910	G	C	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.37;SOR=2.303;VQSLOD=7.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	46826508	rs613870	G	A	2427.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=0.917;VQSLOD=7.01;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,67:67:99:2456,202,0
-chr6	46826715	rs572248	T	A	4133.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=118;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=0.881;VQSLOD=6.50;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,114:114:99:4162,343,0
-chr6	46826844	rs571247	T	C	5230.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=144;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.63;SOR=1.006;VQSLOD=6.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,144:144:99:5259,433,0
-chr6	46826910	rs611779	G	A	4855.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=132;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.04;SOR=1.119;VQSLOD=5.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,132:132:99:4884,397,0
-chr6	46826979	rs9381487	A	G	1623.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.727;ClippingRankSum=-0.199;DB;DP=106;FS=2.830;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.130;POSITIVE_TRAIN_SITE;QD=15.32;ReadPosRankSum=0.117;SOR=1.041;VQSLOD=2.59;culprit=DP	GT:AD:DP:GQ:PL	0/1:54,52:106:99:1652,0,1669
-chr6	46827073	rs547499	A	G	1003.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.612;ClippingRankSum=-0.887;DB;DP=64;FS=0.955;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=-0.699;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.094;SOR=0.831;VQSLOD=2.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:31,33:64:99:1032,0,968
-chr6	46827126	rs610856	C	T	2450.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.98;SOR=0.966;VQSLOD=5.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2479,192,0
-chr6	46827239	rs9395218	C	T	1247.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.769;ClippingRankSum=-0.087;DB;DP=83;FS=13.228;MLEAC=1;MLEAF=0.500;MQ=51.70;MQ0=0;MQRankSum=0.844;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=1.346;SOR=0.158;VQSLOD=1.45;culprit=FS	GT:AD:DP:GQ:PL	0/1:39,44:83:99:1276,0,1186
-chr6	46828670	rs540727	A	G	1780.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.96;SOR=4.804;VQSLOD=6.53;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1809,138,0
-chr6	46830243	rs483813	T	C	95.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=8.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	46832536	rs531049	T	C	161.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.38;SOR=3.611;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:190,15,0
-chr6	46832553	rs530990	A	G	80.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=2.833;VQSLOD=8.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:108,9,0
-chr6	46832642	rs615677	A	C	985.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.43;SOR=6.593;VQSLOD=7.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,26:26:78:1014,78,0
-chr6	46832741	rs529201	T	C	4511.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=123;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.57;SOR=3.352;VQSLOD=5.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,123:123:99:4540,368,0
-chr6	46832813	rs614826	G	A	3006.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.723;ClippingRankSum=-0.748;DB;DP=234;FS=8.321;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=1.246;POSITIVE_TRAIN_SITE;QD=12.85;ReadPosRankSum=1.650;SOR=1.157;VQSLOD=1.43;culprit=FS	GT:AD:DP:GQ:PL	0/1:127,107:234:99:3035,0,4266
-chr6	46834473	rs586986	T	G	189.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.86;SOR=3.611;VQSLOD=5.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:218,15,0
-chr6	46834685	rs586024	G	A	4443.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=121;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.50;SOR=1.857;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,121:121:99:4472,364,0
-chr6	46834906	rs5875987	TG	T	2501.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.68;SOR=3.007;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2539,205,0
-chr6	46836406	rs665551	G	C	117.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.26;SOR=3.258;VQSLOD=5.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:145,12,0
-chr6	46836995	rs515866	T	C	146.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.38;SOR=3.611;VQSLOD=6.79;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,5:5:15:175,15,0
-chr6	46839435	rs58989382	T	C	406.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.854;ClippingRankSum=-0.174;DB;DP=24;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.927;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=2.202;SOR=0.859;VQSLOD=4.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:11,13:24:99:435,0,357
-chr6	46841306	rs220675	T	C	195.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.97;SOR=0.941;VQSLOD=5.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:224,21,0
-chr6	46846277	rs220668	G	A	565.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.42;SOR=5.549;VQSLOD=6.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,15:15:45:594,45,0
-chr6	46847501	rs2273265	T	G	803.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.965;ClippingRankSum=0.700;DB;DP=55;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.735;POSITIVE_TRAIN_SITE;QD=14.61;ReadPosRankSum=1.889;SOR=1.223;VQSLOD=5.17;culprit=FS	GT:AD:DP:GQ:PL	0/1:31,23:54:99:832,0,1017
-chr6	46849057	rs11760108	G	T	191.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.980;ClippingRankSum=0.068;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=0.299;POSITIVE_TRAIN_SITE;QD=12.78;ReadPosRankSum=0.201;SOR=0.693;VQSLOD=6.72;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,7:14:99:220,0,248
-chr6	46852193	rs220663	C	T	254.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.99;SOR=4.174;VQSLOD=7.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:283,21,0
-chr6	46855734	.	C	CAGGGAAGAGGACCCAGTAGTTTATCTGCCCA	53.70	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	46856100	rs678312	G	A	5756.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=152;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.73;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.10;SOR=1.091;VQSLOD=6.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,152:152:99:5785,457,0
-chr6	46858081	rs9472896	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=7.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	46867717	rs220702	C	T	2958.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.40;SOR=3.316;VQSLOD=6.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,78:78:99:2987,235,0
-chr6	46867898	rs3215601	TA	T	1316.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.26;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.12;SOR=5.892;VQSLOD=4.96;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1354,114,0
-chr6	46869895	rs220698	T	G	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	46874325	rs114267112	T	G	1871.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.381;ClippingRankSum=1.525;DB;DP=109;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.943;POSITIVE_TRAIN_SITE;QD=17.17;ReadPosRankSum=2.083;SOR=0.752;VQSLOD=2.72;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:53,56:109:99:1900,0,1690
-chr6	46895158	rs6458530	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	46928378	rs2396803	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46929606	rs1889578	T	C	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	46931019	rs4714972	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46932290	rs9472940	T	C	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:32:40,0,32
-chr6	46935422	rs9296519	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	46980115	rs1226479	G	A	103.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.036;ClippingRankSum=0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=10.38;ReadPosRankSum=0.741;SOR=0.412;VQSLOD=6.30;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,4:10:99:132,0,220
-chr6	46986916	rs1226496	G	A	100.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.01;SOR=1.609;VQSLOD=8.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:128,12,0
-chr6	47015046	rs1352665	G	T	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	47029819	rs945217	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47037438	rs1226539	G	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	47079304	rs10948329	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47106677	.	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47116726	rs2003031	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=26.37;SOR=2.303;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	47163022	rs76480727	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47176242	rs11368956	C	CA	44.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	47200360	.	AAC	A	225.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-0.751;QD=12.54;ReadPosRankSum=-0.751;SOR=3.056;VQSLOD=4.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,11:12:4:212,0,4
-chr6	47200703	rs202137000	A	C	155.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.080;ClippingRankSum=0.291;DB;DP=89;FS=88.069;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-0.508;QD=1.75;ReadPosRankSum=-1.601;SOR=6.868;VQSLOD=-1.420e+01;culprit=FS	GT:AD:DP:GQ:PL	0/1:59,30:89:99:184,0,1744
-chr6	47228836	rs4715001	C	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	47228912	rs10807350	G	A	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.68;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	47369341	rs4301296	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47373447	rs1931826	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47425273	rs1889494	T	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	47450481	rs9395261	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47462615	rs2184398	T	C	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	47464881	rs62410680	G	A	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=23.04;SOR=2.833;VQSLOD=7.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	47464883	rs202187543	G	GT	98.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	47467043	rs34508069	A	ATG	34.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=0.693;VQSLOD=7.53;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
-chr6	47470146	rs1564926	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47489866	rs62410686	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47494842	rs35617629	T	TC	24.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=8.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	47512229	rs6915993	C	T	472.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.902;ClippingRankSum=-1.520;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.645;POSITIVE_TRAIN_SITE;QD=16.88;ReadPosRankSum=-0.369;SOR=0.836;VQSLOD=5.04;culprit=FS	GT:AD:DP:GQ:PL	0/1:13,15:28:99:501,0,447
-chr6	47512590	rs6916578	C	T	344.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.172;ClippingRankSum=-0.793;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.340;POSITIVE_TRAIN_SITE;QD=21.55;ReadPosRankSum=-0.566;SOR=1.609;VQSLOD=6.22;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,11:16:99:373,0,169
-chr6	47522357	rs9473132	G	A	2114.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.279;ClippingRankSum=0.098;DB;DP=140;FS=1.431;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.117;POSITIVE_TRAIN_SITE;QD=15.11;ReadPosRankSum=-0.616;SOR=0.874;VQSLOD=2.05;culprit=DP	GT:AD:DP:GQ:PL	0/1:66,74:140:99:2143,0,2115
-chr6	47530422	rs9395277	A	C	559.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.99;SOR=5.549;VQSLOD=6.68;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,15:15:45:588,45,0
-chr6	47532683	rs9395278	T	A	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.00;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	47545058	rs978448	C	T	76.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.988;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,3:6:99:105,0,105
-chr6	47548672	rs1014001	C	A	2124.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.361;ClippingRankSum=1.150;DB;DP=186;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=1.434;POSITIVE_TRAIN_SITE;QD=11.42;ReadPosRankSum=-1.001;SOR=0.701;VQSLOD=1.41;culprit=FS	GT:AD:DP:GQ:PL	0/1:112,73:185:99:2153,0,3635
-chr6	47549586	rs6926592	A	T	31.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.47;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=3.53;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.09;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,2:4:60:60,0,65
-chr6	47549883	rs2275446	T	C	1040.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.815;ClippingRankSum=-1.023;DB;DP=59;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.902;POSITIVE_TRAIN_SITE;QD=17.64;ReadPosRankSum=1.327;SOR=1.609;VQSLOD=5.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:30,29:59:99:1069,0,967
-chr6	47563692	rs2039503	C	T	15612.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=434;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.86;SOR=1.288;VQSLOD=0.729;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,433:433:99:15641,1302,0
-chr6	47577064	rs9395287	G	A	1930.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.080;ClippingRankSum=-0.414;DB;DP=155;FS=5.202;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=1.011;POSITIVE_TRAIN_SITE;QD=12.46;ReadPosRankSum=1.551;SOR=0.345;VQSLOD=2.02;culprit=DP	GT:AD:DP:GQ:PL	0/1:89,66:155:99:1959,0,2911
-chr6	47591856	rs10948368	T	C	837.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.469;ClippingRankSum=1.334;DB;DP=42;FS=3.025;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.826;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=1.309;SOR=0.151;VQSLOD=2.32;culprit=QD	GT:AD:DP:GQ:PL	0/1:18,24:42:99:866,0,595
-chr6	47592328	rs11309569	GT	G	75.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	47611404	rs13196954	C	G	36.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.937;ClippingRankSum=0.000;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=5.25;ReadPosRankSum=0.937;SOR=0.446;VQSLOD=4.88;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,3:7:65:65,0,111
-chr6	47611442	rs7766527	T	C	84.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-0.421;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.017;POSITIVE_TRAIN_SITE;QD=10.60;ReadPosRankSum=0.421;SOR=1.609;VQSLOD=4.55;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:113,0,102
-chr6	47624115	rs1485782	C	T	140.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=20.11;ReadPosRankSum=1.495;SOR=1.609;VQSLOD=5.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,5:7:57:169,0,57
-chr6	47624129	rs1485783	G	A	221.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=0;MQRankSum=-0.480;POSITIVE_TRAIN_SITE;QD=22.18;ReadPosRankSum=0.480;SOR=2.303;VQSLOD=5.41;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,8:10:57:250,0,57
-chr6	47624239	rs1485784	A	G	779.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.260;ClippingRankSum=-1.087;DB;DP=42;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=-0.455;POSITIVE_TRAIN_SITE;QD=18.57;ReadPosRankSum=-1.744;SOR=0.286;VQSLOD=5.10;culprit=FS	GT:AD:DP:GQ:PL	0/1:19,23:42:99:808,0,614
-chr6	47624299	rs9369730	A	G	990.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.981;ClippingRankSum=0.405;DB;DP=68;FS=2.459;MLEAC=1;MLEAF=0.500;MQ=56.52;MQ0=0;MQRankSum=-0.459;POSITIVE_TRAIN_SITE;QD=14.57;ReadPosRankSum=2.549;SOR=0.389;VQSLOD=2.90;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:29,35:64:99:1019,0,894
-chr6	47624633	rs1021231	G	A	201.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.04;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.64;SOR=3.912;VQSLOD=7.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:18:230,18,0
-chr6	47626149	rs6934553	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47626490	rs10456129	G	C	47.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=15.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.40;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:30:76,0,30
-chr6	47626685	rs6935668	C	T	505.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.678;ClippingRankSum=-0.091;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.677;POSITIVE_TRAIN_SITE;QD=10.12;ReadPosRankSum=-0.677;SOR=0.670;VQSLOD=4.29;culprit=FS	GT:AD:DP:GQ:PL	0/1:32,18:50:99:534,0,1085
-chr6	47626833	rs12201065	C	A	1126.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.697;ClippingRankSum=-0.211;DB;DP=79;FS=1.842;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.624;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=2.098;SOR=0.509;VQSLOD=3.19;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:42,37:79:99:1155,0,1430
-chr6	47631622	rs2396829	G	T	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	47641307	rs1411049	G	C	1221.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.168;ClippingRankSum=0.230;DB;DP=74;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.479;POSITIVE_TRAIN_SITE;QD=16.51;ReadPosRankSum=-0.340;SOR=1.061;VQSLOD=4.74;culprit=FS	GT:AD:DP:GQ:PL	0/1:31,43:74:99:1250,0,1019
-chr6	47645772	rs9369734	G	T	131.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;ClippingRankSum=-0.717;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=1.186;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=1.031;SOR=0.551;VQSLOD=4.95;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,5:11:99:160,0,198
-chr6	47646468	rs6929227	T	C	36.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.87;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:33:65,0,33
-chr6	47646842	rs6907125	A	G	1474.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.856;ClippingRankSum=0.375;DB;DP=112;FS=1.527;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.670;POSITIVE_TRAIN_SITE;QD=13.17;ReadPosRankSum=-0.351;SOR=0.896;VQSLOD=2.99;culprit=DP	GT:AD:DP:GQ:PL	0/1:57,54:111:99:1503,0,1770
-chr6	47647004	rs6911739	C	T	236.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.835;ClippingRankSum=-0.289;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.536;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=0.289;SOR=0.495;VQSLOD=6.19;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,8:12:99:265,0,101
-chr6	47647593	rs58870329	GA	G	32.74	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.91;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.02;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:30:70,0,30
-chr6	47649222	rs8180544	T	G	3766.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.617;ClippingRankSum=-0.635;DB;DP=262;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.348;POSITIVE_TRAIN_SITE;QD=14.38;ReadPosRankSum=1.474;SOR=0.706;VQSLOD=1.98;culprit=FS	GT:AD:DP:GQ:PL	0/1:130,131:261:99:3795,0,4054
-chr6	47649265	rs17541107	T	A	4039.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.520;ClippingRankSum=0.331;DB;DP=283;FS=5.506;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.377;POSITIVE_TRAIN_SITE;QD=14.27;ReadPosRankSum=1.570;SOR=0.994;VQSLOD=1.83;culprit=DP	GT:AD:DP:GQ:PL	0/1:148,135:283:99:4068,0,4356
-chr6	47649573	rs10807371	C	T	3884.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.363;ClippingRankSum=0.166;DB;DP=210;FS=0.513;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=18.50;ReadPosRankSum=2.787;SOR=0.633;VQSLOD=1.64;culprit=FS	GT:AD:DP:GQ:PL	0/1:110,99:209:99:3913,0,7372
-chr6	47649574	rs10807372	A	G	3884.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.254;ClippingRankSum=0.771;DB;DP=211;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=18.41;ReadPosRankSum=2.423;SOR=0.713;VQSLOD=1.59;culprit=FS	GT:AD:DP:GQ:PL	0/1:108,102:210:99:3913,0,7372
-chr6	47649694	rs9381594	A	G	2384.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;ClippingRankSum=0.797;DB;DP=160;FS=5.307;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.869;POSITIVE_TRAIN_SITE;QD=14.90;ReadPosRankSum=0.046;SOR=1.179;VQSLOD=2.22;culprit=DP	GT:AD:DP:GQ:PL	0/1:82,78:160:99:2413,0,2636
-chr6	47653485	rs9369736	A	G	580.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.376;ClippingRankSum=-0.637;DB;DP=39;FS=6.870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.099;POSITIVE_TRAIN_SITE;QD=14.89;ReadPosRankSum=1.119;SOR=2.200;VQSLOD=2.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:22,17:39:99:609,0,665
-chr6	47653536	rs9381596	A	G	676.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;ClippingRankSum=-1.699;DB;DP=50;FS=5.655;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.621;POSITIVE_TRAIN_SITE;QD=13.54;ReadPosRankSum=1.097;SOR=1.197;VQSLOD=1.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:26,24:50:99:705,0,787
-chr6	47654591	rs10948376	G	T	642.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.972;ClippingRankSum=-0.822;DB;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.782;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=-0.752;SOR=1.085;VQSLOD=3.73;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:14,20:34:99:671,0,497
-chr6	47654662	rs10485315	A	G	2893.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=7.315;ClippingRankSum=0.398;DB;DP=167;FS=1.004;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=17.33;ReadPosRankSum=2.188;SOR=0.957;VQSLOD=2.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:84,83:167:99:2922,0,2748
-chr6	47654742	rs9296573	A	T	4359.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.866;ClippingRankSum=0.983;DB;DP=296;FS=5.331;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.493;POSITIVE_TRAIN_SITE;QD=14.73;ReadPosRankSum=-1.261;SOR=0.468;VQSLOD=1.31;culprit=DP	GT:AD:DP:GQ:PL	0/1:143,153:296:99:4388,0,4431
-chr6	47654817	rs1556133	C	A	3193.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.266;ClippingRankSum=-0.767;DB;DP=141;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.607;POSITIVE_TRAIN_SITE;QD=22.65;ReadPosRankSum=0.439;SOR=0.716;VQSLOD=2.57;culprit=FS	GT:AD:DP:GQ:PL	0/1:57,84:141:99:3222,0,2060
-chr6	47654831	rs1556132	A	G	3144.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.124;ClippingRankSum=-0.737;DB;DP=121;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.550;POSITIVE_TRAIN_SITE;QD=25.99;ReadPosRankSum=0.045;SOR=0.730;VQSLOD=2.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:47,74:121:99:3173,0,1780
-chr6	47654864	rs1556131	T	G	1356.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.916;ClippingRankSum=1.761;DB;DP=69;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.023;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.030;SOR=0.980;VQSLOD=4.41;culprit=FS	GT:AD:DP:GQ:PL	0/1:30,39:69:99:1385,0,976
-chr6	47661115	rs6901702	T	C	90.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=2.833;VQSLOD=7.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:118,9,0
-chr6	47661248	rs36010404	AG	A	335.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.98;SOR=4.977;VQSLOD=6.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,11:11:33:373,33,0
-chr6	47661260	rs200900695	AC	A	126.76	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.589;ClippingRankSum=-0.354;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.65;MQ0=0;MQRankSum=-1.768;POSITIVE_TRAIN_SITE;QD=7.92;ReadPosRankSum=1.061;SOR=2.494;VQSLOD=4.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,9:11:22:164,0,22
-chr6	47661387	rs9395311	A	G	2320.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.015;ClippingRankSum=-0.577;DB;DP=139;FS=8.901;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.615;POSITIVE_TRAIN_SITE;QD=16.70;ReadPosRankSum=2.635;SOR=0.237;VQSLOD=1.11;culprit=FS	GT:AD:DP:GQ:PL	0/1:64,75:139:99:2349,0,1921
-chr6	47675922	rs16876334	C	T	1527.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.988;ClippingRankSum=-0.373;DB;DP=82;FS=4.427;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.181;POSITIVE_TRAIN_SITE;QD=18.63;ReadPosRankSum=0.624;SOR=1.413;VQSLOD=1.23;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:37,45:82:99:1556,0,1063
-chr6	47676150	rs9369737	C	T	269.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;ClippingRankSum=1.732;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.283;POSITIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=-0.346;SOR=0.368;VQSLOD=5.18;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,9:23:99:298,0,504
-chr6	47678455	rs11356177	CT	C	1687.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.012;ClippingRankSum=-0.222;DB;DP=162;FS=0.656;MLEAC=1;MLEAF=0.500;MQ=60.33;MQ0=0;MQRankSum=1.477;POSITIVE_TRAIN_SITE;QD=10.42;ReadPosRankSum=0.632;SOR=0.809;VQSLOD=1.77;culprit=FS	GT:AD:DP:GQ:PL	0/1:80,76:156:99:1725,0,2007
-chr6	47678678	rs944056	C	G	3493.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.59;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.34;SOR=2.758;VQSLOD=7.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3522,271,0
-chr6	47678718	rs1318391	C	G	857.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.618;ClippingRankSum=0.693;DB;DP=61;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.080;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.970;SOR=0.439;VQSLOD=5.75;culprit=FS	GT:AD:DP:GQ:PL	0/1:35,26:61:99:886,0,1329
-chr6	47678848	rs199503700	CAA	C	43.74	PASS	AC=1;AF=0.500;AN=2;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.87;SOR=2.303;VQSLOD=8.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:0,2:2:25:81,0,25
-chr6	47678861	rs9381602	A	G	52.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.93;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:25:81,0,25
-chr6	47680450	rs871654	A	C	516.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.618;ClippingRankSum=-0.634;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.410;POSITIVE_TRAIN_SITE;QD=24.61;ReadPosRankSum=0.634;SOR=1.508;VQSLOD=5.59;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:545,0,211
-chr6	47681494	rs6916562	T	C	3414.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.90;SOR=5.235;VQSLOD=6.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3443,259,0
-chr6	47682604	rs9369738	A	C	6287.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=181;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.74;SOR=1.468;VQSLOD=6.07;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,179:179:99:6316,538,0
-chr6	47682949	rs16876369	C	T	1708.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.057;ClippingRankSum=-0.481;DB;DP=110;FS=7.189;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.072;POSITIVE_TRAIN_SITE;QD=15.53;ReadPosRankSum=0.146;SOR=1.458;VQSLOD=1.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:54,56:110:99:1737,0,1465
-chr6	47683057	rs41452951	A	G	376.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;ClippingRankSum=-0.209;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=0.070;POSITIVE_TRAIN_SITE;QD=13.46;ReadPosRankSum=0.070;SOR=0.460;VQSLOD=5.39;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,12:28:99:405,0,546
-chr6	47684591	rs1360157	G	A	2096.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.035;ClippingRankSum=0.291;DB;DP=146;FS=1.305;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.615;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.971;SOR=0.572;VQSLOD=3.15;culprit=DP	GT:AD:DP:GQ:PL	0/1:74,71:145:99:2125,0,2159
-chr6	47686101	rs6914013	T	C	9061.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=255;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.19;SOR=1.281;VQSLOD=5.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,254:254:99:9090,763,0
-chr6	47686235	rs11754756	C	A	1895.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.892;ClippingRankSum=1.540;DB;DP=110;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.867;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.771;SOR=0.905;VQSLOD=3.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:50,60:110:99:1924,0,1695
-chr6	47686397	rs11476874	AT	A	63.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=62.13;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=12.75;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:66:101,0,66
-chr6	47690579	rs1329522	T	C	91.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.76;SOR=0.693;VQSLOD=6.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:119,12,0
-chr6	47690601	rs35597357	T	C	29.77	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=7.44;ReadPosRankSum=0.000;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:37:58,0,37
-chr6	47690613	rs1329523	G	A	81.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.179;VQSLOD=8.50;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:109,9,0
-chr6	47696780	rs2282337	C	T	36.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;ClippingRankSum=-0.720;DB;DP=6;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=6.13;ReadPosRankSum=-0.720;SOR=2.303;VQSLOD=2.06;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,2:6:65:65,0,81
-chr6	47698280	rs1329540	G	A	94.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	47698303	rs1329539	C	T	94.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=7.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	47703969	rs949680	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47707247	rs72864549	C	T	37.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=6.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:65,6,0
-chr6	47708230	rs12199415	A	G	96.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	47708267	rs9473166	C	T	93.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=6.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	47712313	rs9349429	T	G	41.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.87;SOR=2.303;VQSLOD=8.76;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	47714073	rs9367302	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47720533	rs61744507	G	A	144.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.876;ClippingRankSum=-1.652;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.361;POSITIVE_TRAIN_SITE;QD=16.09;ReadPosRankSum=1.881;SOR=0.892;VQSLOD=5.73;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:173,0,134
-chr6	47720824	rs2039141	A	G	2982.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.60;SOR=1.697;VQSLOD=5.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3011,247,0
-chr6	47740398	rs1329529	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47746444	rs10485318	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47749539	rs9395320	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	47749728	rs7741473	T	G	1371.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.498;ClippingRankSum=1.007;DB;DP=64;FS=3.910;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.168;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=-0.210;SOR=0.253;VQSLOD=2.29;culprit=QD	GT:AD:DP:GQ:PL	0/1:23,41:64:99:1400,0,654
-chr6	47754498	rs1329543	A	G	352.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.647;ClippingRankSum=-0.208;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.052;POSITIVE_TRAIN_SITE;QD=13.57;ReadPosRankSum=0.052;SOR=0.446;VQSLOD=5.83;culprit=FS	GT:AD:DP:GQ:PL	0/1:15,11:26:99:381,0,529
-chr6	47754538	rs6900985	T	C	166.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.859;ClippingRankSum=-1.156;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.653;POSITIVE_TRAIN_SITE;QD=9.81;ReadPosRankSum=0.653;SOR=0.293;VQSLOD=5.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:11,6:17:99:195,0,378
-chr6	47763514	rs139235050	TCACACA	T	98.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.10;MQ0=0;QD=19.65;SOR=2.833;VQSLOD=6.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	47808012	rs474725	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47822105	rs532671	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47826378	rs476873	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47841953	rs4715047	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47845813	rs1887899	G	T	171.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=7.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:200,15,0
-chr6	47847179	rs3799276	A	G	11221.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=302;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.02;SOR=1.221;VQSLOD=2.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,301:301:99:11250,905,0
-chr6	47847401	rs2068006	A	G	6414.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=184;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.86;SOR=0.832;VQSLOD=4.02;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,182:182:99:6443,547,0
-chr6	47847683	rs9367307	A	T	3379.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=142;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.80;SOR=3.095;VQSLOD=3.37;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,121:121:99:3408,364,0
-chr6	47862643	rs113155505	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47865882	rs4715053	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47869426	rs1360080	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	47869448	rs1360081	G	A	125.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.26;SOR=1.609;VQSLOD=7.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:153,12,0
-chr6	47871871	rs13194591	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	47871877	.	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	47927739	.	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47941339	rs2753188	G	A	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	47954722	rs2145363	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	47977018	rs2753194	C	A	684.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.070;ClippingRankSum=1.380;DB;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.995;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=1.508;SOR=1.061;VQSLOD=4.96;culprit=FS	GT:AD:DP:GQ:PL	0/1:15,21:36:99:713,0,543
-chr6	47977136	rs45599036	C	T	79.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=19.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.45;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:26:108,0,26
-chr6	48005879	rs12205869	G	A	45.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=9.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	48009812	.	A	C	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	48015295	rs618543	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48015693	rs332554	A	G	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	48026377	rs647942	A	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	48032884	rs75735764	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48036051	rs201541883	A	C	779.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.322;ClippingRankSum=-0.178;DB;DP=120;FS=165.662;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-0.683;QD=6.50;ReadPosRankSum=-4.265;SOR=8.379;VQSLOD=-6.204e+01;culprit=FS	GT:AD:DP:GQ:PL	0/1:52,65:117:99:808,0,1315
-chr6	48083008	rs6908563	G	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	48117685	rs12523977	C	G	501.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;ClippingRankSum=0.073;DB;DP=38;FS=1.785;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.833;POSITIVE_TRAIN_SITE;QD=13.20;ReadPosRankSum=-2.675;SOR=1.329;VQSLOD=1.85;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:20,18:38:99:530,0,640
-chr6	48131753	rs1331118	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48172099	.	G	GGGA	46.70	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=23.35;SOR=0.693;VQSLOD=5.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	48195386	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48214766	rs2456916	A	G	38.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:33:67,0,33
-chr6	48214812	rs2503669	C	G	78.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.754;ClippingRankSum=0.937;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.550;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=11.25;ReadPosRankSum=1.300;SOR=2.775;VQSLOD=0.030;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,3:7:99:107,0,141
-chr6	48214977	rs2503670	A	G	44.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.19;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.40;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:71:73,0,71
-chr6	48215008	rs2496375	G	A	41.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=10.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.07;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:70:70,0,71
-chr6	48225108	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48262773	rs13202212	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48282517	rs11758955	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48282542	rs545090	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48396334	rs9473361	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48445933	rs1121646	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48448275	rs9473387	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48449928	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48450548	rs9784854	G	A	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=7.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	48456067	rs148792649	CAGTCTTGAAGACAAAATGCTAACATGTAATAAGAAAATATTTGA	C	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=7.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	48456290	rs7754822	G	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	48456315	rs9473391	A	T	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	48464593	rs9473403	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48467616	rs12206390	A	G	65.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=1.179;VQSLOD=8.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:93,9,0
-chr6	48468120	rs6915049	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48592097	.	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48596846	rs2912621	T	G	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	48609036	rs963049	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48615474	rs2433657	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48750072	rs2495881	T	C	75.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.09;SOR=2.833;VQSLOD=7.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:103,9,0
-chr6	48792612	rs2495863	C	T	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	48811854	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48825657	rs1938202	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48899692	rs10948458	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	48919773	rs16878430	G	A	235.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.540;ClippingRankSum=-0.212;DB;DP=16;FS=4.467;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.318;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-1.059;SOR=0.525;VQSLOD=3.12;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:7,9:16:99:264,0,243
-chr6	48920376	rs12204534	C	T	96.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=2.833;VQSLOD=7.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	49011686	rs35984632	A	AT	50.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=16.75;SOR=1.179;VQSLOD=7.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:87,9,0
-chr6	49022228	rs6458657	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49036510	rs12194577	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49045630	rs9367346	A	T	789.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.471;ClippingRankSum=-1.379;DB;DP=53;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.098;POSITIVE_TRAIN_SITE;QD=14.90;ReadPosRankSum=2.233;SOR=0.793;VQSLOD=5.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,26:53:99:818,0,792
-chr6	49052341	rs6458676	A	G	38.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=7.75;ReadPosRankSum=-0.358;SOR=1.179;VQSLOD=5.43;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,3:5:34:67,0,34
-chr6	49083404	.	A	G	43.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=10.94;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=3.54;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:61:72,0,61
-chr6	49169185	rs113197207	C	CTTCT	77.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.53;SOR=0.693;VQSLOD=8.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:9:114,9,0
-chr6	49199384	rs570913	T	G	15.65	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	49209747	rs9463466	G	T	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	49212193	rs492254	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49218084	rs7756663	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49218093	rs11453208	A	AT	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=6.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49397107	.	A	G	12.06	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:26:40,0,26
-chr6	49414272	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49415351	.	TA	T	91.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.540;ClippingRankSum=-0.501;DP=115;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=0.642;POSITIVE_TRAIN_SITE;QD=0.80;ReadPosRankSum=0.146;SOR=0.653;VQSLOD=3.81;culprit=FS	GT:AD:DP:GQ:PL	0/1:57,17:74:99:129,0,1146
-chr6	49437853	rs11333073	AT	A	27.74	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.412;ClippingRankSum=-0.483;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=0.985;QD=0.55;ReadPosRankSum=0.770;SOR=0.976	GT:AD:DP:GQ:PL	0/1:38,8:46:65:65,0,808
-chr6	49456545	rs2501965	G	A	816.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.39;SOR=6.273;VQSLOD=4.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,22:22:66:845,66,0
-chr6	49459978	rs2501968	A	G	4668.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=126;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.981;VQSLOD=6.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,124:124:99:4697,373,0
-chr6	49460152	rs1471539	A	G	177.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.65;SOR=3.611;VQSLOD=5.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:206,15,0
-chr6	49479750	rs13193063	T	C	340.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.40;SOR=1.445;VQSLOD=6.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,12:12:36:369,36,0
-chr6	49479775	rs1480615	A	T	224.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.11;SOR=2.584;VQSLOD=7.65;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:253,21,0
-chr6	49480339	rs9463493	A	G	64.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	49494241	rs9367359	A	G	3361.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=95;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.60;SOR=0.826;VQSLOD=7.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,94:94:99:3390,283,0
-chr6	49495862	rs6458696	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49497461	rs2396905	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49508103	rs9463500	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49515525	rs4715136	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49518914	rs6919674	C	G	44.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=2.303;VQSLOD=8.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:72,6,0
-chr6	49522920	.	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49528183	rs6899583	A	G	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	49537956	rs36081197	T	A	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	49559793	rs10948514	G	T	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	49596219	rs4711931	T	C	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	49646966	rs7763840	T	C	66.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=8.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	49650193	rs148454607	CCCT	C	84.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=62.13;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=6.11;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:37:122,0,37
-chr6	49660418	rs12624	A	C	1647.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;ClippingRankSum=-1.338;DB;DP=95;FS=5.883;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=-1.323;POSITIVE_TRAIN_SITE;QD=17.34;ReadPosRankSum=0.011;SOR=1.333;VQSLOD=1.55;culprit=FS	GT:AD:DP:GQ:PL	0/1:42,53:95:99:1676,0,1201
-chr6	49663465	rs2248263	G	A	603.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.236;ClippingRankSum=0.133;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.399;POSITIVE_TRAIN_SITE;QD=18.30;ReadPosRankSum=0.589;SOR=0.957;VQSLOD=5.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,18:32:99:632,0,410
-chr6	49665120	rs10548881	GGT	G	34.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=2.303;VQSLOD=8.54;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
-chr6	49666381	rs515257	G	A	145.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.886;ClippingRankSum=-1.798;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=7.67;ReadPosRankSum=1.184;SOR=0.223;VQSLOD=5.06;culprit=QD	GT:AD:DP:GQ:PL	0/1:13,6:19:99:174,0,478
-chr6	49668405	rs57295760	T	G	1149.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.101;ClippingRankSum=0.570;DB;DP=174;FS=322.757;MLEAC=1;MLEAF=0.500;MQ=47.79;MQ0=0;MQRankSum=-5.344;QD=6.61;ReadPosRankSum=-6.450;SOR=9.149;VQSLOD=-2.485e+02;culprit=FS	GT:AD:DP:GQ:PL	0/1:77,96:173:99:1178,0,1978
-chr6	49676536	rs699954	C	T	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	49693598	rs1068276	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49693612	rs35883674	CT	C	93.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.08;SOR=1.179;VQSLOD=8.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	49695232	rs510770	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49701439	rs1864312	C	A	1555.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;ClippingRankSum=0.346;DB;DP=113;FS=1.849;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.795;POSITIVE_TRAIN_SITE;QD=13.77;ReadPosRankSum=1.613;SOR=0.978;VQSLOD=2.84;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:63,49:112:99:1584,0,2066
-chr6	49701523	rs495335	A	G	1861.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.084;ClippingRankSum=-0.565;DB;DP=149;FS=0.622;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.400;POSITIVE_TRAIN_SITE;QD=12.50;ReadPosRankSum=3.925;SOR=0.775;VQSLOD=2.06;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:84,65:149:99:1890,0,2674
-chr6	49703027	rs3823210	G	T	73.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=14.75;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=6.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:72:102,0,72
-chr6	49787315	rs5876131	G	GT	25.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.86;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:62,6,0
-chr6	49798102	.	C	CAGAG	53.70	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=4.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	49803370	rs1652094	A	G	290.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.34;SOR=4.407;VQSLOD=6.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:319,24,0
-chr6	49807422	rs7753886	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49815873	rs373553362	AT	A	85.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.243;ClippingRankSum=-0.384;DB;DP=85;FS=2.397;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=1.200;QD=1.01;ReadPosRankSum=0.512;SOR=1.508;VQSLOD=1.09;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:52,14:66:99:123,0,1132
-chr6	49818670	rs780782	T	C	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.96;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	49835335	rs1084051	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	49858594	rs2153575	C	T	361.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.037;ClippingRankSum=1.977;DB;DP=21;FS=4.722;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.037;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.336;SOR=0.127;VQSLOD=3.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:390,0,186
-chr6	49913981	rs7760672	C	T	1758.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.016;ClippingRankSum=0.747;DB;DP=119;FS=1.762;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=0.359;POSITIVE_TRAIN_SITE;QD=14.78;ReadPosRankSum=-0.178;SOR=0.963;VQSLOD=3.22;culprit=DP	GT:AD:DP:GQ:PL	0/1:58,61:119:99:1787,0,1869
-chr6	49917264	rs9369926	A	C	219.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.220;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.732;POSITIVE_TRAIN_SITE;QD=12.93;ReadPosRankSum=1.317;SOR=0.425;VQSLOD=5.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,7:17:99:248,0,336
-chr6	49956510	.	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50045305	rs1324514	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50064359	rs9395549	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50087752	rs6458721	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50155014	.	T	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:29:40,0,29
-chr6	50155159	rs700005	A	C	44.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=0.693;VQSLOD=8.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:72,6,0
-chr6	50158759	rs142079970	G	GT	21.73	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0
-chr6	50164244	rs9369936	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50169217	rs148924218	C	CT	19.75	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:56,6,0
-chr6	50197539	rs6910805	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50222518	rs1340844	T	C	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	50225593	rs9349526	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50230041	rs1596084	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50230068	rs7756066	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50231408	rs6903689	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50261294	rs2792835	T	C	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	50265655	rs5876165	GA	G	21.73	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=10.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0
-chr6	50294995	rs10637978	A	ATAATT	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	50298895	rs7775569	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50325057	rs2131281	G	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.10;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	50362460	rs7745382	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50364398	rs6930590	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50366720	rs7738992	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50650700	rs537362	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50805942	rs2817404	T	G	938.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.85;SOR=6.358;VQSLOD=6.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,23:23:69:967,69,0
-chr6	50810497	rs1569778	T	C	85.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.43;SOR=2.833;VQSLOD=7.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:113,9,0
-chr6	50811241	rs2982621	T	A	306.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=4.615;VQSLOD=5.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:27:335,27,0
-chr6	50812003	rs35732696	TA	T	11.99	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=4.00;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	50824804	rs2817423	T	A	1009.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=6.666;VQSLOD=5.96;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,27:27:81:1038,81,0
-chr6	50866066	rs11754505	C	T	130.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.51;SOR=1.609;VQSLOD=7.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:158,12,0
-chr6	50880250	rs61678343	C	CT	116.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.73;MQ0=0;QD=16.70;SOR=3.611;VQSLOD=5.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:154,15,0
-chr6	50886019	rs75756982	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.50;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	50966615	rs557411	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51003728	rs140549964	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51003757	.	T	A	62.74	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51003762	rs145721769	T	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51162298	rs1409888	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51171408	rs1327265	G	A	95.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=9.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	51173538	rs2256042	G	A	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.75;SOR=1.179;VQSLOD=8.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	51173541	rs2256041	A	G	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.80;SOR=1.179;VQSLOD=8.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	51199224	rs2796913	T	C	136.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.38;SOR=1.981;VQSLOD=6.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:165,15,0
-chr6	51274751	.	CTT	C	59.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.550;ClippingRankSum=1.300;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.10;MQ0=0;MQRankSum=-0.937;QD=5.43;ReadPosRankSum=0.550;SOR=0.223;VQSLOD=4.67;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:51:97,0,51
-chr6	51317602	rs9367432	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51329696	rs3928895	G	C	93.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	51339492	rs4090367	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51434479	rs4997737	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.32;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51434483	rs181171044	A	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51446475	rs2495854	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51492046	rs9474033	T	G	2499.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.45;SOR=8.287;VQSLOD=5.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2528,187,0
-chr6	51492164	rs9370040	T	A	258.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.68;SOR=4.174;VQSLOD=6.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:287,21,0
-chr6	51503597	.	C	CAAA	667.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.313;ClippingRankSum=-1.388;DP=300;FS=6.792;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=0;MQRankSum=-2.762;NEGATIVE_TRAIN_SITE;QD=2.23;ReadPosRankSum=-2.418;SOR=0.016;VQSLOD=-2.167e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:77,45:122:99:705,0,1544
-chr6	51512707	rs2580009	T	C	944.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.22;SOR=6.593;VQSLOD=5.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,26:26:78:973,78,0
-chr6	51521787	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51523739	rs115072237	T	C	6637.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=176;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.68;SOR=2.371;VQSLOD=5.00;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,175:175:99:6666,526,0
-chr6	51551346	rs557398	T	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	51590078	rs1326610	T	C	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	51604677	.	C	T	956.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.698;ClippingRankSum=-0.058;DP=66;FS=6.929;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.341;QD=14.50;ReadPosRankSum=1.938;SOR=0.066;VQSLOD=0.460;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,30:66:99:985,0,1262
-chr6	51606225	rs142928645	C	T	114.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-1.380;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.380;POSITIVE_TRAIN_SITE;QD=19.13;ReadPosRankSum=0.720;SOR=1.329;VQSLOD=4.76;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:59:143,0,59
-chr6	51611733	rs200125913	A	C	194.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.113;ClippingRankSum=1.133;DB;DP=24;FS=9.938;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=-0.153;NEGATIVE_TRAIN_SITE;QD=8.12;ReadPosRankSum=0.643;SOR=3.990;VQSLOD=-1.655e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:8,16:24:99:223,0,155
-chr6	51617800	rs1326607	A	G	332.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.28;SOR=4.804;VQSLOD=6.82;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,10:10:30:361,30,0
-chr6	51634407	.	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51640751	rs3920621	C	G	1527.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.616;ClippingRankSum=-0.475;DB;DP=114;FS=5.314;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-1.120;POSITIVE_TRAIN_SITE;QD=13.40;ReadPosRankSum=-0.393;SOR=0.217;VQSLOD=1.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:63,49:112:99:1556,0,2311
-chr6	51649062	rs11435548	G	GT	58.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.42;SOR=1.179;VQSLOD=7.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:95,9,0
-chr6	51649079	rs4715232	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=7.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	51652585	rs1326561	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=7.54;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51652595	rs1326562	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51655796	rs6904634	T	C	99.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.93;SOR=2.303;VQSLOD=6.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:9:127,9,0
-chr6	51655803	rs6924716	C	T	99.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=2.833;VQSLOD=7.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:127,9,0
-chr6	51656236	rs7765455	G	T	1483.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.49;SOR=3.611;VQSLOD=5.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1512,120,0
-chr6	51656388	rs4715233	A	G	93.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	51664791	rs1980834	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51664816	rs2148459	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51671321	rs1326584	T	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	51671350	rs4470847	C	G	66.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=9.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	51673939	rs1326588	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51706167	rs10648630	C	CCCTTT	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.90;SOR=0.693;VQSLOD=8.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51712492	rs9370067	A	T	1705.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.14;SOR=7.523;VQSLOD=6.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1734,126,0
-chr6	51718857	rs1831015	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51720838	rs9349603	T	C	7371.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=189;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.858;VQSLOD=4.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,185:185:99:7400,557,0
-chr6	51720872	rs7452724	A	G	6199.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=161;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.66;SOR=3.188;VQSLOD=6.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,161:161:99:6228,484,0
-chr6	51723015	rs9370074	G	A	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=7.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	51732598	rs9382043	G	A	2712.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.50;SOR=3.026;VQSLOD=5.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,74:74:99:2741,222,0
-chr6	51732628	rs9382044	G	A	3330.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.80;SOR=2.276;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3359,267,0
-chr6	51735261	rs982874	G	T	2752.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.40;SOR=4.558;VQSLOD=6.00;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2781,220,0
-chr6	51735613	rs2064871	T	C	314.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.95;SOR=4.407;VQSLOD=6.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:343,24,0
-chr6	51747589	rs6458801	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51750563	rs4711985	A	T	498.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.32;SOR=5.283;VQSLOD=6.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,13:13:39:527,39,0
-chr6	51757014	rs1321516	C	T	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	51768630	rs141063789	CATATAT	C	229.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.71;MQ0=0;POSITIVE_TRAIN_SITE;QD=10.44;SOR=2.303;VQSLOD=6.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:20:267,20,0
-chr6	51791091	rs4711990	G	T	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	51793425	rs5876244	C	CA	44.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	51796751	rs3857602	G	A	89.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=1.179;VQSLOD=5.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:117,9,0
-chr6	51798753	rs1266888	G	A	308.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.90;SOR=4.407;VQSLOD=6.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:337,24,0
-chr6	51798760	rs1884953	T	A	94.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=9.48;ReadPosRankSum=-0.365;SOR=0.412;VQSLOD=6.15;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,4:10:99:123,0,204
-chr6	51799166	rs1266889	T	C	1497.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.26;SOR=4.977;VQSLOD=5.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,37:37:99:1526,111,0
-chr6	51800445	rs1266890	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51814216	rs4715264	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51814217	rs1266913	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	51844368	rs2435324	A	G	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	51856374	rs9463746	A	G	45.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	51875250	rs2435322	A	C	4902.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=132;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=1.170;VQSLOD=5.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,130:130:99:4931,391,0
-chr6	51882075	rs9349614	C	G	29.77	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.067;ClippingRankSum=0.572;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.589;QD=3.31;ReadPosRankSum=0.572;SOR=0.169	GT:AD:DP:GQ:PL	0/1:6,2:8:58:58,0,201
-chr6	51889483	rs45517932	G	A	1402.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.623;ClippingRankSum=-0.441;DB;DP=91;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.758;QD=15.42;ReadPosRankSum=0.099;SOR=0.684;VQSLOD=3.39;culprit=FS	GT:AD:DP:GQ:PL	0/1:47,44:91:99:1431,0,1559
-chr6	51890823	rs9296669	G	A	908.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.796;ClippingRankSum=-1.279;DB;DP=60;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=0.614;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=0.052;SOR=0.575;VQSLOD=5.85;culprit=FS	GT:AD:DP:GQ:PL	0/1:30,30:60:99:937,0,937
-chr6	51891011	rs2499480	T	C	1469.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.480;ClippingRankSum=1.669;DB;DP=99;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.671;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=0.425;SOR=0.787;VQSLOD=5.12;culprit=FS	GT:AD:DP:GQ:PL	0/1:54,45:99:99:1498,0,1703
-chr6	51913240	rs10948667	G	A	2227.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.872;ClippingRankSum=0.978;DB;DP=133;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.127;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=0.314;SOR=0.691;VQSLOD=4.01;culprit=FS	GT:AD:DP:GQ:PL	0/1:61,72:133:99:2256,0,2006
-chr6	51914898	rs9395759	T	C	962.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.45;SOR=5.211;VQSLOD=6.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,27:27:81:991,81,0
-chr6	51914956	rs9370096	G	A	738.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.924;ClippingRankSum=-1.239;DB;DP=57;FS=1.721;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-2.997;POSITIVE_TRAIN_SITE;QD=12.96;ReadPosRankSum=0.567;SOR=1.274;VQSLOD=0.740;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:30,27:57:99:767,0,838
-chr6	51917550	rs1896983	G	A	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	51923569	rs56342114	CTCTA	C	188.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.74;SOR=3.611;VQSLOD=5.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:16:226,16,0
-chr6	51924774	rs1896976	A	G	11214.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=307;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.73;SOR=0.923;VQSLOD=3.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,306:306:99:11243,918,0
-chr6	51927683	rs13198604	T	C	130.79	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=21.80;ReadPosRankSum=0.736;SOR=0.941;VQSLOD=5.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,5:6:22:159,0,22
-chr6	51930886	rs5876252	T	TA	1123.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.558;ClippingRankSum=0.596;DB;DP=98;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.066;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.047;SOR=1.571;VQSLOD=5.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,49:63:99:1161,0,109
-chr6	51935061	rs4711996	T	G	632.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.75;SOR=5.670;VQSLOD=6.32;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:661,48,0
-chr6	51935747	rs17576809	C	T	1555.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.681;ClippingRankSum=0.579;DB;DP=78;FS=1.884;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=2.282;SOR=1.437;VQSLOD=1.66;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:34,44:78:99:1584,0,1003
-chr6	51936846	rs3936986	T	C	1197.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.520;ClippingRankSum=2.065;DB;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.165;POSITIVE_TRAIN_SITE;QD=18.43;ReadPosRankSum=-0.310;SOR=0.499;VQSLOD=5.41;culprit=FS	GT:AD:DP:GQ:PL	0/1:29,36:65:99:1226,0,894
-chr6	51938242	rs9474140	A	G	2915.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.879;ClippingRankSum=-1.660;DB;DP=204;FS=1.266;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.616;POSITIVE_TRAIN_SITE;QD=14.29;ReadPosRankSum=0.116;SOR=0.846;VQSLOD=2.35;culprit=DP	GT:AD:DP:GQ:PL	0/1:112,92:204:99:2944,0,3367
-chr6	51944847	rs1892274	T	C	1304.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.941;ClippingRankSum=0.488;DB;DP=91;FS=6.922;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.933;POSITIVE_TRAIN_SITE;QD=14.34;ReadPosRankSum=0.242;SOR=2.140;VQSLOD=2.08;culprit=FS	GT:AD:DP:GQ:PL	0/1:45,46:91:99:1333,0,1431
-chr6	51946893	rs6458806	T	C	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	51947237	rs9474143	G	A	5131.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;ClippingRankSum=0.221;DB;DP=273;FS=2.813;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.398;POSITIVE_TRAIN_SITE;QD=18.80;ReadPosRankSum=1.871;SOR=0.538;VQSLOD=1.29;culprit=DP	GT:AD:DP:GQ:PL	0/1:114,158:272:99:5160,0,3305
-chr6	51949862	rs9370097	A	G	953.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.068;ClippingRankSum=-1.115;DB;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.363;POSITIVE_TRAIN_SITE;QD=14.67;ReadPosRankSum=-0.917;SOR=0.505;VQSLOD=5.49;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,29:65:99:982,0,1231
-chr6	51953191	rs6905678	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51963443	rs6914462	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	51971195	rs3997006	T	C	91.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=7.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	51997155	rs1892278	A	C	327.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.056;VQSLOD=5.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:27:356,27,0
-chr6	52054249	rs7747909	G	A	105.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.421;ClippingRankSum=0.922;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.017;POSITIVE_TRAIN_SITE;QD=13.22;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=4.45;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:134,0,134
-chr6	52061133	rs11962054	A	G	16.63	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.63;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	52064989	rs11755816	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52065009	rs11751159	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52073500	rs4464776	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52075816	rs2397079	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=9.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	52085748	rs591274	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52111808	rs761167	C	T	630.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.571;ClippingRankSum=-0.018;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.792;POSITIVE_TRAIN_SITE;QD=19.11;ReadPosRankSum=0.534;SOR=0.743;VQSLOD=5.64;culprit=FS	GT:AD:DP:GQ:PL	0/1:13,20:33:99:659,0,402
-chr6	52117224	rs604952	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52129484	rs2230240	C	T	3990.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.023;ClippingRankSum=-0.723;DB;DP=236;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.012;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.682;SOR=0.712;VQSLOD=1.85;culprit=FS	GT:AD:DP:GQ:PL	0/1:105,131:236:99:4019,0,2992
-chr6	52129667	rs2307326	G	A	917.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.356;ClippingRankSum=-0.312;DB;DP=53;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.791;POSITIVE_TRAIN_SITE;QD=17.32;ReadPosRankSum=-2.147;SOR=0.808;VQSLOD=3.93;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:25,28:53:99:946,0,873
-chr6	52130745	rs6925229	T	C	162.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.139;ClippingRankSum=1.898;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=10.17;ReadPosRankSum=0.597;SOR=0.340;VQSLOD=6.23;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,6:16:99:191,0,354
-chr6	52131254	rs10807441	C	T	1383.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.953;ClippingRankSum=0.770;DB;DP=83;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.223;POSITIVE_TRAIN_SITE;QD=16.67;ReadPosRankSum=0.269;SOR=1.534;VQSLOD=5.05;culprit=FS	GT:AD:DP:GQ:PL	0/1:43,40:83:99:1412,0,1442
-chr6	52137313	rs12207056	C	T	464.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.684;ClippingRankSum=-0.306;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.56;MQ0=0;MQRankSum=-0.162;POSITIVE_TRAIN_SITE;QD=14.08;ReadPosRankSum=1.207;SOR=1.609;VQSLOD=5.72;culprit=FS	GT:AD:DP:GQ:PL	0/1:17,16:33:99:493,0,518
-chr6	52138441	rs6918669	G	A	286.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.355;ClippingRankSum=-0.442;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.971;SOR=1.781;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,9:18:99:315,0,267
-chr6	52141670	rs3765446	A	T	142.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.635;ClippingRankSum=1.000;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.134;POSITIVE_TRAIN_SITE;QD=11.90;ReadPosRankSum=0.135;SOR=1.371;VQSLOD=6.12;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,5:12:99:171,0,247
-chr6	52142092	rs2307325	C	T	222.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;ClippingRankSum=0.092;DB;DP=24;FS=1.999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.276;POSITIVE_TRAIN_SITE;QD=9.28;ReadPosRankSum=0.704;SOR=1.214;VQSLOD=2.73;culprit=QD	GT:AD:DP:GQ:PL	0/1:16,8:24:99:251,0,540
-chr6	52142582	rs13191372	G	A	424.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.394;ClippingRankSum=0.496;DB;DP=31;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=13.70;ReadPosRankSum=1.409;SOR=0.527;VQSLOD=5.12;culprit=FS	GT:AD:DP:GQ:PL	0/1:17,14:31:99:453,0,593
-chr6	52143987	rs2076510	C	T	232.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;ClippingRankSum=-0.625;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.241;POSITIVE_TRAIN_SITE;QD=13.69;ReadPosRankSum=1.973;SOR=0.593;VQSLOD=5.87;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,8:17:99:261,0,314
-chr6	52144081	rs2073036	T	C	952.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;ClippingRankSum=-0.724;DB;DP=63;FS=1.092;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.193;POSITIVE_TRAIN_SITE;QD=15.12;ReadPosRankSum=0.145;SOR=0.485;VQSLOD=2.82;culprit=FS	GT:AD:DP:GQ:PL	0/1:29,34:63:99:981,0,911
-chr6	52147271	rs7756989	T	C	20.80	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=1.380;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.720;QD=3.47;ReadPosRankSum=0.720;SOR=0.693	GT:AD:DP:GQ:PL	0/1:4,2:6:49:49,0,109
-chr6	52147363	rs12202495	A	G	191.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.279;ClippingRankSum=0.579;DB;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.193;POSITIVE_TRAIN_SITE;QD=9.59;ReadPosRankSum=1.042;SOR=0.392;VQSLOD=5.45;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,8:20:99:220,0,424
-chr6	52147692	rs2307322	T	A	893.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.042;ClippingRankSum=0.160;DB;DP=47;FS=9.107;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.460;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=3.166;SOR=2.472;VQSLOD=0.472;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:22,25:47:99:922,0,588
-chr6	52148465	rs9474192	T	G	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.21;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	52217185	rs9395785	C	G	142.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.922;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.495;POSITIVE_TRAIN_SITE;QD=20.40;ReadPosRankSum=0.922;SOR=1.609;VQSLOD=5.94;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,5:7:66:171,0,66
-chr6	52240487	rs6458837	G	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	52245945	rs71794438	CA	C	38.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=2.303;VQSLOD=7.53;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	52257835	rs669893	A	G	17.61	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.61;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:44,3,0
-chr6	52257856	rs526553	G	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	52267967	rs76408349	A	C	39.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=1.231;POSITIVE_TRAIN_SITE;QD=7.95;ReadPosRankSum=-0.358;SOR=0.446;VQSLOD=5.70;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,2:5:68:68,0,92
-chr6	52268008	rs3748066	T	G	117.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=16.82;ReadPosRankSum=-0.922;SOR=0.527;VQSLOD=6.33;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,5:7:62:146,0,62
-chr6	52268086	rs146353145	C	T	319.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;ClippingRankSum=-0.387;DB;DP=21;FS=3.222;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-0.810;QD=15.23;ReadPosRankSum=0.599;SOR=1.911;VQSLOD=1.55;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,11:21:99:348,0,301
-chr6	52268890	rs17591381	G	A	546.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.060;ClippingRankSum=0.774;DB;DP=49;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=1.035;POSITIVE_TRAIN_SITE;QD=11.16;ReadPosRankSum=0.794;SOR=0.712;VQSLOD=5.57;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,22:49:99:575,0,819
-chr6	52269199	rs3799272	T	C	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	52296461	rs1840169	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52319251	rs614570	C	T	274.18	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.751;POSITIVE_TRAIN_SITE;QD=30.46;ReadPosRankSum=0.751;SOR=3.056;VQSLOD=5.38;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,8:9:10:302,0,10
-chr6	52355206	rs2273120	T	C	1095.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.353;VQSLOD=6.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,29:29:87:1124,87,0
-chr6	52357260	rs7757370	C	A	601.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.84;SOR=5.670;VQSLOD=6.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:630,48,0
-chr6	52367845	rs3032	C	T	381.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.028;ClippingRankSum=0.927;DB;DP=24;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=15.91;ReadPosRankSum=-0.348;SOR=0.859;VQSLOD=5.92;culprit=FS	GT:AD:DP:GQ:PL	0/1:11,13:24:99:410,0,338
-chr6	52370939	rs9688915	G	A	1148.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.520;ClippingRankSum=1.052;DB;DP=64;FS=1.426;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.175;POSITIVE_TRAIN_SITE;QD=17.95;ReadPosRankSum=0.836;SOR=1.212;VQSLOD=2.70;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:29,35:64:99:1177,0,853
-chr6	52380641	rs941968	C	T	424.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.390;ClippingRankSum=-1.102;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.603;SOR=0.576;VQSLOD=5.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,14:30:99:453,0,559
-chr6	52381728	rs6917085	A	T	86.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=-0.727;SOR=1.609;VQSLOD=6.10;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:32:115,0,32
-chr6	52425189	rs7744675	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52433894	rs55959984	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52451301	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52453985	rs9370135	T	A	42.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:30:71,0,30
-chr6	52469904	rs9463802	A	G	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	52475696	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52483058	rs11755043	C	A	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.10;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	52538160	rs55704840	A	AG	38.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	52538171	rs7746344	A	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	52538198	rs9349638	T	A	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=0.693;VQSLOD=7.10;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	52538242	rs9349639	T	G	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=7.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	52538390	rs9349640	T	C	45.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=8.54;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	52541811	rs13211066	G	A	2092.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=7.941;VQSLOD=6.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2121,157,0
-chr6	52546789	rs2281484	C	T	1421.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.25;SOR=7.328;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1450,114,0
-chr6	52553436	rs9382133	C	T	766.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;ClippingRankSum=0.060;DB;DP=45;FS=4.452;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.370;POSITIVE_TRAIN_SITE;QD=17.04;ReadPosRankSum=0.418;SOR=1.118;VQSLOD=2.96;culprit=FS	GT:AD:DP:GQ:PL	0/1:18,26:44:99:795,0,532
-chr6	52565427	rs4637643	T	G	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	52568775	rs6909894	G	C	181.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=1.981;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:210,15,0
-chr6	52568848	rs36098646	G	GA	25.95	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=62.65;MQ0=0;MQRankSum=0.727;QD=6.49;ReadPosRankSum=0.727;SOR=0.916	GT:AD:DP:GQ:PL	0/1:1,3:4:13:63,0,13
-chr6	52615371	rs199546282	T	G	302.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.160;ClippingRankSum=-0.230;DB;DP=163;FS=296.910;MLEAC=1;MLEAF=0.500;MQ=54.98;MQ0=0;MQRankSum=-0.947;QD=1.86;ReadPosRankSum=-4.824;SOR=8.189;VQSLOD=-1.995e+02;culprit=FS	GT:AD:DP:GQ:PL	0/1:103,59:162:99:331,0,2945
-chr6	52616633	rs72934249	C	T	667.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.954;ClippingRankSum=0.781;DB;DP=47;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.909;POSITIVE_TRAIN_SITE;QD=14.21;ReadPosRankSum=-0.631;SOR=0.509;VQSLOD=5.18;culprit=FS	GT:AD:DP:GQ:PL	0/1:26,21:47:99:696,0,789
-chr6	52617731	rs2180314	C	G	6239.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.736;ClippingRankSum=-0.690;DB;DP=405;FS=1.200;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-0.793;POSITIVE_TRAIN_SITE;QD=15.41;ReadPosRankSum=1.185;SOR=0.583;VQSLOD=1.22;culprit=DP	GT:AD:DP:GQ:PL	0/1:207,197:404:99:6268,0,6969
-chr6	52622475	rs2608624	G	T	277.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.387;ClippingRankSum=-0.529;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.529;POSITIVE_TRAIN_SITE;QD=17.36;ReadPosRankSum=-1.482;SOR=0.941;VQSLOD=4.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,9:16:99:306,0,255
-chr6	52622814	rs2254050	C	T	889.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.466;ClippingRankSum=2.068;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.456;POSITIVE_TRAIN_SITE;QD=17.80;ReadPosRankSum=0.651;SOR=0.773;VQSLOD=5.34;culprit=FS	GT:AD:DP:GQ:PL	0/1:24,26:50:99:918,0,713
-chr6	52630153	rs6458868	C	T	560.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.030;ClippingRankSum=-0.430;DB;DP=42;FS=1.283;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=0.483;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=2.308;SOR=1.064;VQSLOD=2.33;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:21,20:41:99:589,0,560
-chr6	52630269	rs6458869	C	A	534.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.861;ClippingRankSum=-1.139;DB;DP=26;FS=1.757;MLEAC=1;MLEAF=0.500;MQ=49.59;MQ0=0;MQRankSum=-2.083;POSITIVE_TRAIN_SITE;QD=20.57;ReadPosRankSum=-0.583;SOR=0.346;VQSLOD=1.61;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:8,18:26:99:563,0,197
-chr6	52631188	rs2749029	A	G	696.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.911;ClippingRankSum=0.581;DB;DP=58;FS=2.243;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.722;POSITIVE_TRAIN_SITE;QD=12.01;ReadPosRankSum=0.581;SOR=0.416;VQSLOD=2.99;culprit=QD	GT:AD:DP:GQ:PL	0/1:33,25:58:99:725,0,1078
-chr6	52655827	rs6904269	G	A	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=9.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	52657321	rs4147615	T	C	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.21;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	52658962	rs1051775	T	C	16388.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.00;AN=2;BaseQRankSum=1.724;ClippingRankSum=-0.564;DB;DP=430;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;MQRankSum=0.177;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=26.20;ReadPosRankSum=0.878;SOR=0.736;VQSLOD=-8.417e-01;culprit=DP	GT:AD:DP:GQ:PL	1/1:1,429:430:99:16417,1283,0
-chr6	52660828	rs2894803	C	A	2866.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=8.608;VQSLOD=6.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2895,220,0
-chr6	52661267	.	ATATATATATATATATATATATGTGTG	A	235.79	PASS	AC=2;AF=1.00;AN=2;DP=21;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.56;MQ0=0;QD=11.23;SOR=3.912;VQSLOD=4.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:19:273,19,0
-chr6	52662263	rs2397106	C	T	1326.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=34.02;SOR=5.892;VQSLOD=5.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1355,114,0
-chr6	52662568	rs139503836	G	A	365.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.392;ClippingRankSum=-0.198;DB;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-1.778;QD=10.16;ReadPosRankSum=1.120;SOR=0.293;VQSLOD=2.34;culprit=FS	GT:AD:DP:GQ:PL	0/1:23,13:36:99:394,0,797
-chr6	52663705	rs9349644	C	T	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	52663813	rs10948722	A	G	801.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=6.091;VQSLOD=6.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,20:20:60:830,60,0
-chr6	52664133	.	T	C	1090.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.013;ClippingRankSum=-0.873;DP=57;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.328;QD=19.14;ReadPosRankSum=0.377;SOR=0.285;VQSLOD=3.89;culprit=FS	GT:AD:DP:GQ:PL	0/1:26,31:57:99:1119,0,874
-chr6	52670630	rs10807454	A	C	691.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.81;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.23;SOR=3.258;VQSLOD=6.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:720,48,0
-chr6	52670633	rs62412861	A	G	725.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.81;MQ0=0;QD=24.12;SOR=3.258;VQSLOD=4.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:51:754,51,0
-chr6	52670639	rs62412870	C	T	680.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.44;MQ0=0;QD=29.35;SOR=3.258;VQSLOD=4.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:709,48,0
-chr6	52677230	rs5876288	G	GA	2040.73	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.420;ClippingRankSum=0.166;DB;DP=129;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=0.381;POSITIVE_TRAIN_SITE;QD=15.82;ReadPosRankSum=-0.674;SOR=1.636;VQSLOD=4.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:6,81:87:99:2070,156,0
-chr6	52678337	rs6458873	G	T	1706.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.330;VQSLOD=6.87;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1735,132,0
-chr6	52678463	rs6458874	C	T	360.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.20;SOR=4.804;VQSLOD=6.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,10:10:30:389,30,0
-chr6	52678500	rs6458875	C	G	82.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.43;SOR=2.833;VQSLOD=8.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:110,9,0
-chr6	52688905	rs2983232	G	T	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.72;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	52694086	rs4311507	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52695461	rs10948726	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.50;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52697601	rs55815585	T	G	3617.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=94;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.68;SOR=2.354;VQSLOD=5.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,92:92:99:3646,277,0
-chr6	52697825	rs4715345	A	C	5351.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=123;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.62;SOR=2.226;VQSLOD=5.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,122:122:99:5380,367,0
-chr6	52697834	rs4715346	C	A	5365.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=120;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.36;SOR=2.507;VQSLOD=5.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,120:120:99:5394,370,0
-chr6	52697890	rs4715347	C	T	2514.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=5.042;VQSLOD=6.95;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,65:65:99:2543,195,0
-chr6	52698035	rs4715348	A	G	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	52698653	rs6458880	C	T	131.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=3.258;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:159,12,0
-chr6	52698788	rs4712021	T	C	3962.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.39;SOR=8.977;VQSLOD=6.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,88:88:99:3991,271,0
-chr6	52698798	rs4715349	G	T	4293.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=99;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.88;SOR=9.210;VQSLOD=6.95;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,99:99:99:4322,298,0
-chr6	52700920	rs2397117	T	C	5074.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=131;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=9.735;VQSLOD=6.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,129:129:99:5103,388,0
-chr6	52701143	rs2397118	C	T	12265.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=338;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.40;SOR=1.526;VQSLOD=2.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,337:337:99:12294,1013,0
-chr6	52701458	rs2397119	T	C	81.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=2.833;VQSLOD=7.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:109,9,0
-chr6	52701582	rs62412887	T	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	52701589	rs2397121	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	52702324	rs4715350	T	C	4926.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=136;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.30;SOR=3.048;VQSLOD=4.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,135:135:99:4955,406,0
-chr6	52702529	rs4715351	T	C	1973.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.80;SOR=7.743;VQSLOD=6.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2002,141,0
-chr6	52712461	rs9296693	G	A	232.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.26;SOR=4.174;VQSLOD=3.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:261,21,0
-chr6	52712645	rs9296694	C	G	4081.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=107;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.14;SOR=2.812;VQSLOD=6.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,107:107:99:4110,322,0
-chr6	52713902	rs62412891	C	T	1799.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.94;SOR=3.958;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1828,141,0
-chr6	52724654	rs9349647	C	T	94.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=2.833;VQSLOD=8.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:122,9,0
-chr6	52735179	rs72938158	T	A	2626.77	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.785;ClippingRankSum=1.186;DB;DP=68;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.577;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.32;ReadPosRankSum=3.323;SOR=5.136;VQSLOD=0.542;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	1/1:4,64:68:99:2655,186,0
-chr6	52743455	rs4715360	T	C	2478.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=8.287;VQSLOD=5.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2507,187,0
-chr6	52744741	rs13198332	G	A	498.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.93;SOR=0.693;VQSLOD=6.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,14:14:42:527,42,0
-chr6	52746642	rs72940404	G	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:30:40,0,30
-chr6	52761898	rs2295605	T	C	585.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.63;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.46;SOR=5.784;VQSLOD=7.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,17:17:51:614,51,0
-chr6	52766192	rs6935603	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52767869	rs542113	T	A	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	52768392	.	CA	C	63.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.806;ClippingRankSum=-0.832;DP=73;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.10;MQ0=0;MQRankSum=1.360;QD=0.87;ReadPosRankSum=-1.466;SOR=0.111;VQSLOD=2.98;culprit=FS	GT:AD:DP:GQ:PL	0/1:42,11:53:99:101,0,838
-chr6	52785560	rs689167	G	A	446.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.37;SOR=0.836;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,13:13:39:475,39,0
-chr6	52785580	rs689197	G	A	546.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.17;SOR=0.693;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:575,48,0
-chr6	52785649	rs581594	G	A	388.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.47;SOR=4.804;VQSLOD=6.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,10:10:30:417,30,0
-chr6	52795274	rs547362	G	T	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	52802244	rs371403	A	G	109.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.26;SOR=1.609;VQSLOD=7.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:137,12,0
-chr6	52820382	rs10948733	G	A	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	52835606	rs571672	T	C	114.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.51;SOR=3.258;VQSLOD=6.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:142,12,0
-chr6	52839185	rs428957	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52843131	rs367836	G	T	2227.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.34;SOR=8.015;VQSLOD=7.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2256,163,0
-chr6	52843477	rs375887	A	G	995.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.52;SOR=5.058;VQSLOD=6.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,25:25:75:1024,75,0
-chr6	52843524	rs543613	T	C	344.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.54;SOR=4.615;VQSLOD=4.87;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:27:373,27,0
-chr6	52847150	rs67390777	TA	T	38.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=66.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=12.75;SOR=2.833;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:75,9,0
-chr6	52847273	rs3831189	T	TAC	756.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.167;ClippingRankSum=0.026;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.26;MQ0=0;MQRankSum=-0.078;POSITIVE_TRAIN_SITE;QD=22.93;ReadPosRankSum=0.544;SOR=2.621;VQSLOD=6.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,24:30:99:794,0,101
-chr6	52847551	rs316133	G	C	3193.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.28;SOR=2.833;VQSLOD=6.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,83:83:99:3222,249,0
-chr6	52847682	rs10557482	GGAGA	G	232.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=62.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=3.912;VQSLOD=6.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:18:270,18,0
-chr6	52849146	rs316128	G	T	959.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.28;SOR=5.136;VQSLOD=6.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,26:26:78:988,78,0
-chr6	52849481	.	C	CT	353.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;ClippingRankSum=-1.730;DP=59;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-0.663;POSITIVE_TRAIN_SITE;QD=6.00;ReadPosRankSum=-1.275;SOR=1.609;VQSLOD=5.78;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,23:37:99:391,0,172
-chr6	52850040	rs669674	A	G	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	52851936	rs508078	T	C	1473.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.45;SOR=5.031;VQSLOD=7.06;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1502,114,0
-chr6	52881235	rs11756408	C	T	143.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.198;POSITIVE_TRAIN_SITE;QD=20.54;ReadPosRankSum=-0.922;SOR=1.609;VQSLOD=5.81;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,5:7:63:172,0,63
-chr6	52892683	rs222456	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52929010	rs11401639	A	AT	12.93	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52938468	.	AT	A	1342.73	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.585;ClippingRankSum=-0.022;DP=99;FS=6.337;MLEAC=2;MLEAF=1.00;MQ=60.68;MQ0=0;MQRankSum=-0.412;POSITIVE_TRAIN_SITE;QD=13.56;ReadPosRankSum=-1.299;SOR=3.952;VQSLOD=1.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:2,62:64:99:1380,141,0
-chr6	52941597	rs34970749	TA	T	32.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.35;SOR=0.693;VQSLOD=7.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	52943841	rs35757290	TA	T	559.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.53;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.10;SOR=5.670;VQSLOD=5.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:597,48,0
-chr6	52958479	rs2816350	A	G	1666.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.21;SOR=3.816;VQSLOD=6.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1695,132,0
-chr6	52962715	rs2744455	C	T	1715.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.20;SOR=6.184;VQSLOD=5.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1744,132,0
-chr6	52985368	rs6919768	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	52992851	rs377590473	AGAAGG	A	35.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.663;ClippingRankSum=1.055;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQ0=0;MQRankSum=-2.362;QD=1.70;ReadPosRankSum=0.280;SOR=0.043;VQSLOD=3.98;culprit=FS	GT:AD:DP:GQ:PL	0/1:18,3:21:73:73,0,1155
-chr6	52998788	rs2816346	G	A	128.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-chr6	52998834	rs2816345	C	T	125.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.247;ClippingRankSum=-0.163;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.054;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.464;SOR=0.307;VQSLOD=5.43;culprit=QD	GT:AD:DP:GQ:PL	0/1:10,6:16:99:154,0,317
-chr6	52998856	rs2518573	T	G	225.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.191;ClippingRankSum=0.439;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=-0.322;POSITIVE_TRAIN_SITE;QD=9.03;ReadPosRankSum=-0.966;SOR=0.412;VQSLOD=4.85;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,10:24:99:254,0,473
-chr6	53010182	rs9367511	A	G	116.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.927;ClippingRankSum=-0.533;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.212;POSITIVE_TRAIN_SITE;QD=8.98;ReadPosRankSum=1.092;SOR=0.368;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	0/1:8,5:13:99:145,0,291
-chr6	53010609	rs59049517	TA	T	57.90	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;ClippingRankSum=0.731;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.53;MQ0=0;MQRankSum=-0.731;POSITIVE_TRAIN_SITE;QD=8.27;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.42;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,4:5:14:95,0,14
-chr6	53061391	rs78303998	G	A	114.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.017;ClippingRankSum=-0.421;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.922;QD=14.35;ReadPosRankSum=0.421;SOR=0.693;VQSLOD=4.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:143,0,121
-chr6	53062469	rs7772870	G	A	98.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=1.179;VQSLOD=7.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:126,9,0
-chr6	53071745	rs77744774	C	T	100.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.480;ClippingRankSum=-1.271;DB;DP=10;FS=6.990;MLEAC=1;MLEAF=0.500;MQ=41.67;MQ0=0;MQRankSum=-1.733;QD=10.08;ReadPosRankSum=0.000;SOR=4.407;VQSLOD=-7.559e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,8:10:38:129,0,38
-chr6	53072388	rs62413047	A	C	120.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;ClippingRankSum=-0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.036;POSITIVE_TRAIN_SITE;QD=12.08;ReadPosRankSum=1.133;SOR=1.329;VQSLOD=4.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,6:10:99:149,0,125
-chr6	53072441	rs11758224	A	G	29.77	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.067;ClippingRankSum=-1.067;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.572;QD=3.72;ReadPosRankSum=-1.067;SOR=0.693	GT:AD:DP:GQ:PL	0/1:6,2:8:58:58,0,221
-chr6	53072501	rs11756086	T	C	22.79	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-1.495;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.198;QD=3.26;ReadPosRankSum=-0.198;SOR=1.802	GT:AD:DP:GQ:PL	0/1:5,2:7:51:51,0,184
-chr6	53103062	rs10583094	TAC	T	36.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.35;SOR=0.693;VQSLOD=8.72;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	53119938	.	G	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	53120011	.	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53173704	rs209484	C	T	29.79	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=9.93;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:25:58,0,25
-chr6	53186203	rs209499	C	T	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	53210951	rs209523	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53229240	rs1346602	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	53302223	rs11967914	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53306308	rs1401156	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53325093	rs11969450	G	A	33.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:34:62,0,34
-chr6	53363487	rs10604357	GGGCT	G	931.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.719;ClippingRankSum=0.942;DB;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-0.356;POSITIVE_TRAIN_SITE;QD=14.33;ReadPosRankSum=0.364;SOR=1.141;VQSLOD=6.29;culprit=FS	GT:AD:DP:GQ:PL	0/1:37,26:63:99:969,0,1920
-chr6	53365019	rs661346	G	C	4389.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=126;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.84;SOR=1.262;VQSLOD=6.97;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,125:125:99:4418,375,0
-chr6	53366008	rs12525473	C	T	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	53366061	rs12525474	C	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	53370107	rs661603	T	C	253.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.678;ClippingRankSum=0.998;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.103;POSITIVE_TRAIN_SITE;QD=15.86;ReadPosRankSum=-0.578;SOR=0.693;VQSLOD=6.35;culprit=FS	GT:AD:DP:GQ:PL	0/1:8,8:16:99:282,0,260
-chr6	53370327	rs17884019	C	T	446.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.961;ClippingRankSum=-0.471;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.300;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=0.848;SOR=1.112;VQSLOD=4.70;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,16:32:99:475,0,461
-chr6	53372145	rs1555903	T	C	760.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.717;ClippingRankSum=-1.830;DB;DP=57;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.171;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=0.024;SOR=0.385;VQSLOD=5.78;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,23:57:99:789,0,1142
-chr6	53373197	rs2235707	G	C	375.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.581;ClippingRankSum=-1.193;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.250;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=0.028;SOR=0.387;VQSLOD=5.68;culprit=FS	GT:AD:DP:GQ:PL	0/1:15,10:25:99:404,0,860
-chr6	53373198	rs17880319	A	G	375.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.380;ClippingRankSum=-0.765;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.716;SOR=0.404;VQSLOD=4.81;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,11:27:99:404,0,860
-chr6	53373276	rs17881410	C	T	1348.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.532;ClippingRankSum=-1.183;DB;DP=82;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.107;POSITIVE_TRAIN_SITE;QD=16.45;ReadPosRankSum=0.654;SOR=0.742;VQSLOD=4.98;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,42:82:99:1377,0,1369
-chr6	53373624	rs3830795	G	GCTCCAC	706.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.129;ClippingRankSum=-1.149;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.77;MQ0=0;MQRankSum=-5.319;POSITIVE_TRAIN_SITE;QD=14.13;ReadPosRankSum=-0.966;SOR=0.399;VQSLOD=1.11;culprit=FS	GT:AD:DP:GQ:PL	0/1:29,20:49:99:744,0,1894
-chr6	53378861	rs11385177	A	AT	433.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;ClippingRankSum=-1.535;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.249;POSITIVE_TRAIN_SITE;QD=14.46;ReadPosRankSum=0.456;SOR=0.693;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:15,15:30:99:471,0,469
-chr6	53379193	rs17885705	A	T	3122.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;ClippingRankSum=-0.402;DB;DP=206;FS=0.540;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.173;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.720;SOR=0.781;VQSLOD=1.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:103,103:206:99:3151,0,3088
-chr6	53379352	rs17881444	A	G	1554.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.383;ClippingRankSum=1.328;DB;DP=104;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=14.95;ReadPosRankSum=1.368;SOR=0.719;VQSLOD=3.93;culprit=FS	GT:AD:DP:GQ:PL	0/1:55,49:104:99:1583,0,1676
-chr6	53379405	rs3736729	A	C	1019.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.536;ClippingRankSum=0.059;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.059;POSITIVE_TRAIN_SITE;QD=20.40;ReadPosRankSum=-1.690;SOR=1.051;VQSLOD=4.96;culprit=FS	GT:AD:DP:GQ:PL	0/1:21,29:50:99:1048,0,693
-chr6	53379499	rs17883806	G	C	182.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.133;ClippingRankSum=-2.383;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.866;POSITIVE_TRAIN_SITE;QD=18.28;ReadPosRankSum=-0.741;SOR=1.085;VQSLOD=5.36;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,6:10:99:211,0,139
-chr6	53385934	rs17883816	T	C	291.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.062;ClippingRankSum=0.766;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.237;POSITIVE_TRAIN_SITE;QD=19.45;ReadPosRankSum=1.591;SOR=1.112;VQSLOD=4.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,9:15:99:320,0,184
-chr6	53394065	rs17883125	C	T	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=7.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	53409451	.	C	CCCT	53.70	PASS	AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=13.43;SOR=2.303;VQSLOD=6.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	53470507	rs9349679	G	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	53493640	rs6925537	T	C	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.13;SOR=1.609;VQSLOD=6.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:83,6,0
-chr6	53493642	rs6903184	G	C	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	53516876	rs6928338	T	G	250.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.13;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.86;SOR=0.892;VQSLOD=6.06;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:27:279,27,0
-chr6	53519062	rs10948758	A	G	5150.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=125;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.87;SOR=0.882;VQSLOD=6.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,125:125:99:5179,376,0
-chr6	53519605	rs3799260	C	T	7091.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=190;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.12;SOR=0.693;VQSLOD=2.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,190:190:99:7120,571,0
-chr6	53519857	rs12210809	G	A	4207.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=112;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=36.51;SOR=1.220;VQSLOD=5.94;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,110:110:99:4236,331,0
-chr6	53520088	rs2038939	T	C	2813.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.28;SOR=3.643;VQSLOD=5.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2842,207,0
-chr6	53520124	rs2038940	A	G	1799.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;MQ0=0;QD=29.97;SOR=6.273;VQSLOD=4.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1828,138,0
-chr6	53528784	rs1326553	A	G	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	53529027	rs1326554	A	T	3242.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=37.30;SOR=4.929;VQSLOD=5.98;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,87:87:99:3271,262,0
-chr6	53543213	rs4541744	C	T	99.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=1.179;VQSLOD=7.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:127,9,0
-chr6	53559094	rs10452610	A	G	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	53586617	rs35610624	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53601883	rs7745277	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53606394	rs4457161	T	C	12.07	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:23:40,0,23
-chr6	53620789	rs7763482	C	T	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=2.303;VQSLOD=9.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	53626319	.	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53654033	rs3001010	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	53662935	rs9382237	C	T	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=6.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	53674284	rs4475321	C	T	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	53676354	rs4715425	G	A	91.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=7.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	53690779	rs3003489	T	C	46.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	53691835	rs7755924	A	G	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	53694407	rs6904545	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53707098	rs4286781	C	T	4179.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=110;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.61;SOR=2.876;VQSLOD=6.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,110:110:99:4208,331,0
-chr6	53723062	rs145334901	AT	A	13.89	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.94;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:50,6,0
-chr6	53726761	rs3935663	C	T	47.79	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.71;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:22:76,0,22
-chr6	53726780	rs3935664	A	G	90.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=1.179;VQSLOD=9.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:118,9,0
-chr6	53749074	rs4265034	G	C	79.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.43;SOR=2.833;VQSLOD=8.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:107,9,0
-chr6	53755300	rs6458972	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53762210	rs62397108	C	A	270.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.681;ClippingRankSum=-0.033;DB;DP=23;FS=4.904;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.824;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.890;SOR=2.165;VQSLOD=2.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,10:22:99:299,0,376
-chr6	53764829	rs71558840	T	G	125.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.804;ClippingRankSum=1.304;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.80;MQ0=0;MQRankSum=2.136;QD=4.84;ReadPosRankSum=1.969;SOR=0.387;VQSLOD=1.71;culprit=QD	GT:AD:DP:GQ:PL	0/1:15,10:25:99:154,0,298
-chr6	53778661	rs201915048	T	G	38.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.938;ClippingRankSum=-0.459;DB;DP=84;FS=136.465;MLEAC=1;MLEAF=0.500;MQ=49.90;MQ0=0;MQRankSum=-5.277;QD=0.46;ReadPosRankSum=-6.784;SOR=6.271;VQSLOD=-4.291e+01;culprit=FS	GT:AD:DP:GQ:PL	0/1:61,22:83:67:67,0,1974
-chr6	53784268	rs59246960	C	CT	332.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.32;MQ0=0;QD=19.57;SOR=5.549;VQSLOD=4.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,15:15:45:370,45,0
-chr6	53784662	rs3777661	A	G	109.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.000;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:138,0,134
-chr6	53785276	rs2294789	C	A	178.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.383;ClippingRankSum=-0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=17.88;ReadPosRankSum=-2.072;SOR=1.085;VQSLOD=5.18;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:4,6:10:99:207,0,141
-chr6	53785759	rs201940946	G	GT	45.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.550;ClippingRankSum=-0.550;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.34;MQ0=0;MQRankSum=-0.550;QD=5.72;ReadPosRankSum=-0.937;SOR=0.941;VQSLOD=4.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:54:83,0,54
-chr6	53787267	rs2294791	G	C	221.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;ClippingRankSum=1.656;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.935;POSITIVE_TRAIN_SITE;QD=17.06;ReadPosRankSum=0.101;SOR=0.836;VQSLOD=6.75;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,7:13:99:250,0,220
-chr6	53805460	rs6907354	A	G	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	53893735	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53927326	rs4715439	T	C	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	53953083	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53973251	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	53982990	rs4521576	A	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	53986503	rs2145754	A	T	180.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.749;ClippingRankSum=1.186;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.466;POSITIVE_TRAIN_SITE;QD=16.43;ReadPosRankSum=1.932;SOR=0.859;VQSLOD=6.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,6:11:99:209,0,162
-chr6	53989526	rs4712056	G	A	2189.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.153;ClippingRankSum=1.695;DB;DP=131;FS=6.808;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-1.076;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=1.657;SOR=0.326;VQSLOD=1.81;culprit=FS	GT:AD:DP:GQ:PL	0/1:59,70:129:99:2218,0,1820
-chr6	54003899	rs11965480	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	54013765	rs2145755	A	G	923.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.107;ClippingRankSum=0.838;DB;DP=48;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.142;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=0.735;SOR=0.866;VQSLOD=4.39;culprit=FS	GT:AD:DP:GQ:PL	0/1:22,26:48:99:952,0,728
-chr6	54025155	rs10484648	T	C	760.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.724;ClippingRankSum=0.655;DB;DP=56;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-0.099;POSITIVE_TRAIN_SITE;QD=13.59;ReadPosRankSum=0.458;SOR=1.151;VQSLOD=3.37;culprit=FS	GT:AD:DP:GQ:PL	0/1:30,23:53:99:789,0,990
-chr6	54030072	rs1280860	T	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.53;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	54035531	rs2792626	T	C	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=9.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	54046086	rs2792632	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54054686	rs6934690	T	A	2471.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;ClippingRankSum=-2.348;DB;DP=167;FS=1.953;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=14.80;ReadPosRankSum=1.550;SOR=0.892;VQSLOD=2.86;culprit=DP	GT:AD:DP:GQ:PL	0/1:79,88:167:99:2500,0,2110
-chr6	54054837	rs9296739	A	G	811.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.037;ClippingRankSum=-2.468;DB;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.876;POSITIVE_TRAIN_SITE;QD=18.04;ReadPosRankSum=-1.149;SOR=0.829;VQSLOD=5.35;culprit=FS	GT:AD:DP:GQ:PL	0/1:21,24:45:99:840,0,675
-chr6	54058426	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54067088	rs67016420	AT	A	245.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.880;ClippingRankSum=-0.810;DB;DP=24;FS=3.222;MLEAC=1;MLEAF=0.500;MQ=62.65;MQ0=0;MQRankSum=1.303;POSITIVE_TRAIN_SITE;QD=10.24;ReadPosRankSum=0.880;SOR=0.160;VQSLOD=2.56;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:11,10:21:99:283,0,313
-chr6	54095411	rs2275770	C	G	1855.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.478;ClippingRankSum=-0.434;DB;DP=111;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.030;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=-1.101;SOR=0.609;VQSLOD=4.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:58,53:111:99:1884,0,2350
-chr6	54095423	rs816384	T	C	2503.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.058;ClippingRankSum=-0.087;DB;DP=130;FS=7.052;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.073;POSITIVE_TRAIN_SITE;QD=19.26;ReadPosRankSum=0.105;SOR=2.758;VQSLOD=0.745;culprit=FS	GT:AD:DP:GQ:PL	0/1:58,72:130:99:2532,0,2153
-chr6	54095524	rs2275769	C	T	4212.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.148;ClippingRankSum=1.384;DB;DP=307;FS=2.750;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-1.330;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=0.874;SOR=0.887;VQSLOD=1.41;culprit=DP	GT:AD:DP:GQ:PL	0/1:165,138:303:99:4241,0,5117
-chr6	54157748	rs6458990	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54157803	rs149997923	G	GTT	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54157804	rs13211037	A	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54159866	rs7775058	C	T	83.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.76;SOR=1.179;VQSLOD=7.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:111,9,0
-chr6	54159915	rs7740868	G	T	64.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=2.833;VQSLOD=8.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	54166206	.	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54166208	.	CA	C	43.79	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=14.60;SOR=0.223;VQSLOD=4.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:19:81,0,19
-chr6	54173085	rs2297981	T	A	239.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.26;SOR=4.174;VQSLOD=7.06;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:268,21,0
-chr6	54175705	rs148816365	C	CTTTCTT	143	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.37;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.01;SOR=1.609;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:180,12,0
-chr6	54185689	rs2297983	G	T	92.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=2.833;VQSLOD=9.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:120,9,0
-chr6	54186024	rs2297986	T	C	1611.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.67;SOR=5.235;VQSLOD=7.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1640,126,0
-chr6	54186147	rs1058768	T	C	3340.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.94;SOR=0.906;VQSLOD=4.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3369,274,0
-chr6	54191363	rs9370289	G	A	180.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.611;VQSLOD=5.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:209,15,0
-chr6	54191970	rs1848440	T	A	4352.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=121;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.31;SOR=3.556;VQSLOD=5.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,121:121:99:4381,364,0
-chr6	54208353	rs1417387	T	C	185.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.97;SOR=3.912;VQSLOD=6.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:18:214,18,0
-chr6	54212964	rs1876606	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54349833	rs2294725	G	A	95.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017;ClippingRankSum=0.000;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.31;MQ0=0;MQRankSum=0.421;POSITIVE_TRAIN_SITE;QD=11.97;ReadPosRankSum=-1.368;SOR=0.693;VQSLOD=5.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:124,0,121
-chr6	54350048	rs807991	G	A	997.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.754;ClippingRankSum=0.019;DB;DP=73;FS=12.208;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.551;SOR=0.108;VQSLOD=1.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:28,38:66:99:1026,0,963
-chr6	54350422	rs565623	G	A	1056.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;ClippingRankSum=-0.634;DB;DP=67;FS=3.327;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.433;POSITIVE_TRAIN_SITE;QD=15.77;ReadPosRankSum=-1.010;SOR=1.142;VQSLOD=2.92;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:32,35:67:99:1085,0,982
-chr6	54356832	rs3900305	T	A	31.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=6.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=5.26;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,2:5:60:60,0,75
-chr6	54438922	rs10447409	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54467267	rs1951694	A	G	44.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.23;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:73,0,32
-chr6	54477874	rs5876389	T	TA	16.80	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=8.40;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:53,6,0
-chr6	54485844	rs7766941	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54489986	rs10948830	G	A	2797.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.226;ClippingRankSum=-0.973;DB;DP=129;FS=4.335;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.300;NEGATIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=1.119;SOR=0.983;VQSLOD=-1.343e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:54,73:127:99:2826,0,2602
-chr6	54489990	rs10948831	A	G	2774.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.682;ClippingRankSum=-0.704;DB;DP=125;FS=2.332;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.479;POSITIVE_TRAIN_SITE;QD=22.20;ReadPosRankSum=0.468;SOR=0.927;VQSLOD=0.604;culprit=DP	GT:AD:DP:GQ:PL	0/1:52,71:123:99:2803,0,2545
-chr6	54490041	rs9349726	T	C	2720.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.830;ClippingRankSum=-0.591;DB;DP=155;FS=2.034;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=2.054;POSITIVE_TRAIN_SITE;QD=17.55;ReadPosRankSum=0.525;SOR=0.513;VQSLOD=1.47;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:71,82:153:99:2749,0,2148
-chr6	54490338	rs10807475	T	A	832.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.069;ClippingRankSum=-0.537;DB;DP=81;FS=11.744;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.204;POSITIVE_TRAIN_SITE;QD=10.28;ReadPosRankSum=0.105;SOR=0.051;VQSLOD=0.328;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,38:74:99:870,0,1117
-chr6	54500405	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54557514	rs1395632	G	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	54571089	rs6907631	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54635275	rs2397171	G	C	38.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=-0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.720;POSITIVE_TRAIN_SITE;QD=6.46;ReadPosRankSum=0.720;SOR=0.307;VQSLOD=5.95;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,2:6:67:67,0,148
-chr6	54635398	rs5876400	T	TG	256.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.600;ClippingRankSum=-2.000;DB;DP=14;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=51.87;MQ0=0;MQRankSum=-1.733;POSITIVE_TRAIN_SITE;QD=18.34;ReadPosRankSum=-1.467;SOR=1.288;VQSLOD=1.73;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:5,9:14:99:294,0,145
-chr6	54635417	rs4516942	G	A	237.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.532;ClippingRankSum=-0.794;DB;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-1.172;POSITIVE_TRAIN_SITE;QD=11.89;ReadPosRankSum=-0.189;SOR=0.693;VQSLOD=4.98;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,10:20:99:266,0,354
-chr6	54635605	rs73742825	C	G	103.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.07;MQ0=0;QD=17.17;SOR=1.609;VQSLOD=3.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:131,12,0
-chr6	54661634	rs12216186	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	54672835	rs10807480	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54682692	.	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54691959	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54692294	rs72957572	A	G	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	54734941	rs7765721	C	A	557.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.038;ClippingRankSum=-1.807;DB;DP=46;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.312;POSITIVE_TRAIN_SITE;QD=12.13;ReadPosRankSum=0.089;SOR=0.412;VQSLOD=4.55;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,19:46:99:586,0,962
-chr6	54735122	rs1472679	A	G	2623.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.370;ClippingRankSum=-0.594;DB;DP=179;FS=1.203;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.157;POSITIVE_TRAIN_SITE;QD=14.66;ReadPosRankSum=1.205;SOR=0.798;VQSLOD=2.83;culprit=DP	GT:AD:DP:GQ:PL	0/1:91,86:177:99:2652,0,2889
-chr6	54735594	rs995851	G	A	418.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.928;ClippingRankSum=0.395;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.187;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=-0.686;SOR=0.576;VQSLOD=5.25;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:16,14:30:99:447,0,581
-chr6	54735606	rs995852	G	A	893.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.18;SOR=6.358;VQSLOD=6.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,23:23:69:922,69,0
-chr6	54792553	.	G	A	1230.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.237;ClippingRankSum=1.275;DP=82;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.68;MQ0=0;MQRankSum=-1.187;QD=15.01;ReadPosRankSum=-0.624;SOR=1.402;VQSLOD=3.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,48:75:99:1259,0,685
-chr6	54807006	rs171224	T	G	114.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;ClippingRankSum=1.368;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=14.35;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.54;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:143,0,127
-chr6	54824610	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54857680	rs2134536	G	A	45.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=0.988;SOR=0.693;VQSLOD=5.75;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,3:6:73:74,0,73
-chr6	54936685	rs57552002	T	TAATA	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	54938529	rs4312988	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	54998074	rs9370385	A	G	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	55003132	rs9349759	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55028053	rs200898132	CAACA	C	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.60;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=6.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	55028113	rs6459069	C	T	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.60;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	55040774	rs4615392	A	G	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=8.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	55045025	rs9370399	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55113411	rs3122169	C	A	2001.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.942;ClippingRankSum=-1.093;DB;DP=131;FS=4.929;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.196;POSITIVE_TRAIN_SITE;QD=15.28;ReadPosRankSum=-0.937;SOR=1.302;VQSLOD=2.09;culprit=DP	GT:AD:DP:GQ:PL	0/1:65,66:131:99:2030,0,2129
-chr6	55142337	rs2653349	A	G	920.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.329;ClippingRankSum=-0.235;DB;DP=82;FS=3.142;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=0;MQRankSum=0.602;POSITIVE_TRAIN_SITE;QD=11.23;ReadPosRankSum=1.940;SOR=1.110;VQSLOD=2.51;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:47,31:78:99:949,0,1545
-chr6	55142458	rs11455646	C	CT	65.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.309;ClippingRankSum=-1.788;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=0;MQRankSum=0.244;POSITIVE_TRAIN_SITE;QD=2.99;ReadPosRankSum=-0.380;SOR=0.446;VQSLOD=6.64;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,7:14:99:103,0,107
-chr6	55190480	rs12110721	G	A	59.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.76;SOR=1.179;VQSLOD=7.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:87,9,0
-chr6	55196299	rs4715531	C	A	87.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=2.833;VQSLOD=9.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:115,9,0
-chr6	55196587	rs12199003	C	T	2169.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.778;ClippingRankSum=1.972;DB;DP=139;FS=4.029;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.737;POSITIVE_TRAIN_SITE;QD=15.61;ReadPosRankSum=1.585;SOR=0.438;VQSLOD=2.24;culprit=DP	GT:AD:DP:GQ:PL	0/1:67,71:138:99:2198,0,1867
-chr6	55206112	rs7761953	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55215079	rs1032767	G	A	1033.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.33;SOR=5.211;VQSLOD=6.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,27:27:81:1062,81,0
-chr6	55215155	rs7743512	C	T	247.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.106;ClippingRankSum=1.059;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.106;POSITIVE_TRAIN_SITE;QD=15.49;ReadPosRankSum=-1.164;SOR=0.976;VQSLOD=5.41;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,9:16:99:276,0,215
-chr6	55216005	rs870806	G	A	1207.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.265;ClippingRankSum=0.451;DB;DP=75;FS=2.105;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.005;POSITIVE_TRAIN_SITE;QD=16.10;ReadPosRankSum=0.589;SOR=0.234;VQSLOD=3.38;culprit=DP	GT:AD:DP:GQ:PL	0/1:36,39:75:99:1236,0,1296
-chr6	55223501	rs41474045	T	G	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	55223531	rs62419074	A	G	95.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.763;ClippingRankSum=1.110;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.457;POSITIVE_TRAIN_SITE;QD=6.38;ReadPosRankSum=0.457;SOR=0.160;VQSLOD=4.75;culprit=QD	GT:AD:DP:GQ:PL	0/1:11,4:15:99:124,0,384
-chr6	55223962	.	G	GTCTATCTATCTATCTA	839.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.176;ClippingRankSum=1.806;DP=80;FS=1.944;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=0;MQRankSum=-1.121;POSITIVE_TRAIN_SITE;QD=10.50;ReadPosRankSum=-2.584;SOR=0.237;VQSLOD=1.23;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:30,22:52:99:877,0,3184
-chr6	55224107	rs9475257	A	G	80.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.231;POSITIVE_TRAIN_SITE;QD=16.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=5.30;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:65:109,0,65
-chr6	55227565	rs17830060	T	C	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	55227593	rs9475263	C	T	30.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=0.000;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=1.380;POSITIVE_TRAIN_SITE;QD=5.13;ReadPosRankSum=-0.720;SOR=1.179;VQSLOD=5.45;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,2:6:59:59,0,110
-chr6	55227683	rs9475264	C	G	70.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;ClippingRankSum=-0.248;DB;DP=9;FS=3.010;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.573;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.203;SOR=1.911;VQSLOD=1.76;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,3:9:99:99,0,193
-chr6	55227930	rs35444148	CA	C	43.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.42;SOR=2.833;VQSLOD=8.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:80,9,0
-chr6	55258643	rs28479599	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55263789	rs9396088	C	T	128.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.51;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-chr6	55263921	rs41271314	T	C	376.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.406;ClippingRankSum=0.798;DB;DP=32;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.044;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.136;SOR=0.078;VQSLOD=2.13;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:20,12:32:99:405,0,694
-chr6	55264362	rs6936510	T	C	1182.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.65;SOR=6.736;VQSLOD=6.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,28:28:84:1211,84,0
-chr6	55264461	rs6913781	C	T	236.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.83;SOR=4.174;VQSLOD=6.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:265,21,0
-chr6	55266394	rs1546297	T	A	509.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.23;SOR=5.283;VQSLOD=7.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,13:13:39:538,39,0
-chr6	55266625	rs9370418	T	C	5961.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=169;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.73;SOR=1.061;VQSLOD=5.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,169:169:99:5990,508,0
-chr6	55266722	rs12529201	C	T	2018.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.58;SOR=6.593;VQSLOD=6.37;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2047,162,0
-chr6	55266796	rs10948913	C	T	23.79	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.480;QD=2.38;ReadPosRankSum=1.271;SOR=0.105	GT:AD:DP:GQ:PL	0/1:8,2:10:52:52,0,252
-chr6	55275656	rs884360	A	C	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	55294300	rs1393326	T	A	60.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=7.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	55297178	rs1032766	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55334381	rs9382495	G	A	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	55357373	rs4530860	A	G	71.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=6.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	55358360	rs9475318	A	G	91.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=8.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	55359142	rs70986720	A	AC	44.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	55359361	rs62407080	T	A	121.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.467;ClippingRankSum=0.267;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.200;POSITIVE_TRAIN_SITE;QD=8.70;ReadPosRankSum=1.067;SOR=0.307;VQSLOD=4.49;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,5:14:99:150,0,312
-chr6	55360086	rs4538708	A	G	530.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=5.283;VQSLOD=7.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,13:13:39:559,39,0
-chr6	55361878	rs9475319	T	C	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=9.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	55365910	rs59233169	A	ACT	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	55368931	rs4540264	T	C	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	55378633	rs13206666	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	55381262	rs6459082	G	A	5521.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=145;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.70;SOR=4.220;VQSLOD=6.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,145:145:99:5550,436,0
-chr6	55381574	rs9464253	T	G	460.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.44;SOR=5.283;VQSLOD=7.38;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,13:13:39:489,39,0
-chr6	55381594	rs9464254	T	C	300.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.19;SOR=4.407;VQSLOD=7.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:329,24,0
-chr6	55392955	rs7743010	C	G	87.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.13;SOR=0.693;VQSLOD=8.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:9:115,9,0
-chr6	55392956	rs7743274	G	A	87.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=1.179;VQSLOD=7.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:115,9,0
-chr6	55406399	rs9367638	C	T	1374.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.41;SOR=7.223;VQSLOD=6.72;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1403,108,0
-chr6	55425387	rs9367641	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55431875	rs9464265	C	G	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	55471178	rs4583976	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55494744	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55509428	rs4504466	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55519639	rs10807498	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55545792	rs34899952	C	T	572.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.12;SOR=5.549;VQSLOD=6.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,15:15:45:601,45,0
-chr6	55625041	rs3798845	G	A	44.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.67;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:26:73,0,26
-chr6	55714314	rs62404968	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	55730212	rs2021803	G	A	169.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.969;ClippingRankSum=-0.648;DB;DP=22;FS=1.707;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.126;POSITIVE_TRAIN_SITE;QD=7.72;ReadPosRankSum=1.126;SOR=1.179;VQSLOD=2.48;culprit=QD	GT:AD:DP:GQ:PL	0/1:14,8:22:99:198,0,496
-chr6	55739553	rs3734444	A	G	5242.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=7.927;ClippingRankSum=0.832;DB;DP=341;FS=2.501;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=1.703;POSITIVE_TRAIN_SITE;QD=15.37;ReadPosRankSum=0.746;SOR=0.848;VQSLOD=1.42;culprit=DP	GT:AD:DP:GQ:PL	0/1:176,162:338:99:5271,0,5457
-chr6	55848128	rs6911711	C	T	57.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.09;SOR=1.179;VQSLOD=8.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:85,9,0
-chr6	55924214	rs3830813	TC	T	169.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.073;ClippingRankSum=0.583;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.869;POSITIVE_TRAIN_SITE;QD=13.06;ReadPosRankSum=0.779;SOR=0.693;VQSLOD=6.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,6:12:99:207,0,206
-chr6	55926067	rs181810990	T	A	105.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.550;ClippingRankSum=0.550;DB;DP=7;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.550;QD=15.11;ReadPosRankSum=-0.937;SOR=2.494;VQSLOD=1.41;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:3,4:7:92:134,0,92
-chr6	55929347	rs2235735	T	C	2151.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.816;ClippingRankSum=1.043;DB;DP=139;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=1.492;POSITIVE_TRAIN_SITE;QD=15.48;ReadPosRankSum=2.796;SOR=0.714;VQSLOD=2.90;culprit=FS	GT:AD:DP:GQ:PL	0/1:63,75:138:99:2180,0,1872
-chr6	55929582	rs80177427	C	T	195.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.989;ClippingRankSum=0.000;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.264;POSITIVE_TRAIN_SITE;QD=10.88;ReadPosRankSum=-0.996;SOR=0.368;VQSLOD=4.38;culprit=FS	GT:AD:DP:GQ:PL	0/1:11,7:18:99:224,0,344
-chr6	55932035	rs138548441	A	AT	3804.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.471;ClippingRankSum=-0.649;DB;DP=235;FS=5.070;MLEAC=1;MLEAF=0.500;MQ=60.13;MQ0=0;MQRankSum=-0.423;QD=16.19;ReadPosRankSum=-0.407;SOR=1.173;VQSLOD=-7.158e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:134,100:234:99:3842,0,6908
-chr6	55932036	rs62406152	C	T	3813.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.075;ClippingRankSum=1.080;DB;DP=238;FS=5.079;MLEAC=1;MLEAF=0.500;MQ=60.22;MQ0=0;MQRankSum=1.382;QD=16.02;ReadPosRankSum=-0.395;SOR=1.179;VQSLOD=-6.900e-02;culprit=DP	GT:AD:DP:GQ:PL	0/1:136,102:238:99:3842,0,6908
-chr6	55932278	rs12209529	C	T	994.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.948;ClippingRankSum=0.169;DB;DP=74;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.664;POSITIVE_TRAIN_SITE;QD=13.44;ReadPosRankSum=0.071;SOR=0.463;VQSLOD=4.42;culprit=FS	GT:AD:DP:GQ:PL	0/1:42,32:74:99:1023,0,1552
-chr6	55932511	rs9396171	A	G	64.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	55933942	rs12189567	A	G	1295.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.173;ClippingRankSum=0.118;DB;DP=97;FS=4.397;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=13.36;ReadPosRankSum=-0.265;SOR=0.278;VQSLOD=2.33;culprit=DP	GT:AD:DP:GQ:PL	0/1:53,43:96:99:1324,0,1752
-chr6	55933987	rs12189571	A	C	812.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.663;ClippingRankSum=-0.455;DB;DP=59;FS=5.997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.675;POSITIVE_TRAIN_SITE;QD=13.78;ReadPosRankSum=1.539;SOR=2.506;VQSLOD=2.27;culprit=FS	GT:AD:DP:GQ:PL	0/1:33,25:58:99:841,0,1009
-chr6	55935196	rs17218309	G	A	45.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	55935617	rs41271338	T	C	3245.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.630;ClippingRankSum=-1.316;DB;DP=211;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.833;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=-0.759;SOR=0.734;VQSLOD=1.27;culprit=FS	GT:AD:DP:GQ:PL	0/1:104,107:211:99:3274,0,3061
-chr6	55935791	rs1028390	T	C	301.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;ClippingRankSum=1.010;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.780;POSITIVE_TRAIN_SITE;QD=17.75;ReadPosRankSum=-0.241;SOR=0.804;VQSLOD=5.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:8,9:17:99:330,0,267
-chr6	55938839	rs4715576	G	A	104.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.774;ClippingRankSum=-0.099;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.296;POSITIVE_TRAIN_SITE;QD=5.82;ReadPosRankSum=-0.591;SOR=0.616;VQSLOD=4.82;culprit=QD	GT:AD:DP:GQ:PL	0/1:13,5:18:99:133,0,453
-chr6	55942538	rs969513	G	T	175.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=1.022;VQSLOD=6.00;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:204,15,0
-chr6	55942643	rs3065899	CAT	C	36.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.24;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.76;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:41:74,0,41
-chr6	55942956	rs17218770	C	G	1775.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.357;ClippingRankSum=0.320;DB;DP=106;FS=6.993;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=1.655;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=1.003;SOR=0.281;VQSLOD=1.69;culprit=FS	GT:AD:DP:GQ:PL	0/1:50,56:106:99:1804,0,1640
-chr6	55943073	rs76049205	T	C	470.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.873;ClippingRankSum=1.669;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.003;POSITIVE_TRAIN_SITE;QD=21.40;ReadPosRankSum=1.135;SOR=1.085;VQSLOD=4.22;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,13:22:99:499,0,281
-chr6	55943101	rs62404861	C	A	242.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.366;ClippingRankSum=-0.340;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.340;POSITIVE_TRAIN_SITE;QD=16.18;ReadPosRankSum=1.324;SOR=0.818;VQSLOD=5.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,8:15:99:271,0,258
-chr6	55966027	rs12206920	C	G	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	55966418	rs4379279	A	G	640.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=5.670;VQSLOD=6.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,16:16:48:669,48,0
-chr6	55988619	rs41464152	T	C	84.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.19;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=6.50;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:28:113,0,28
-chr6	55988796	rs150586735	TTA	T	665.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.931;ClippingRankSum=-0.589;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.65;MQ0=0;MQRankSum=-1.804;POSITIVE_TRAIN_SITE;QD=20.80;ReadPosRankSum=0.285;SOR=0.957;VQSLOD=5.92;culprit=FS	GT:AD:DP:GQ:PL	0/1:14,18:32:99:703,0,546
-chr6	55988837	.	CT	C	386.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.483;ClippingRankSum=-1.883;DP=57;FS=8.505;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-0.083;POSITIVE_TRAIN_SITE;QD=6.78;ReadPosRankSum=0.276;SOR=2.910;VQSLOD=1.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:15,24:39:99:424,0,248
-chr6	55988932	rs41271844	T	C	1723.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.801;ClippingRankSum=0.515;DB;DP=108;FS=2.530;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=0.871;POSITIVE_TRAIN_SITE;QD=15.96;ReadPosRankSum=0.465;SOR=0.446;VQSLOD=2.59;culprit=DP	GT:AD:DP:GQ:PL	0/1:50,57:107:99:1752,0,1593
-chr6	55989320	rs12210901	T	C	81.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;ClippingRankSum=-0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=13.63;ReadPosRankSum=0.406;SOR=0.693;VQSLOD=6.07;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,3:6:97:110,0,97
-chr6	55990773	rs146607719	GTTTAC	G	82.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=-0.358;POSITIVE_TRAIN_SITE;QD=16.55;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=5.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:99:120,0,131
-chr6	56006672	rs10807510	C	T	2289.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.297;ClippingRankSum=-0.222;DB;DP=137;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.209;POSITIVE_TRAIN_SITE;QD=16.71;ReadPosRankSum=0.316;SOR=0.641;VQSLOD=3.89;culprit=FS	GT:AD:DP:GQ:PL	0/1:67,70:137:99:2318,0,1931
-chr6	56021453	rs33997736	CTA	C	44.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	56021870	rs111577315	T	TAAA	789.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.38;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.23;SOR=5.892;VQSLOD=6.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,18:18:59:827,59,0
-chr6	56021985	rs1925180	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56021991	rs1925181	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56022644	rs9382583	C	T	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	56023811	rs994667	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56029832	rs10708181	AT	A	131.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.64;SOR=3.912;VQSLOD=6.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,6:6:18:169,18,0
-chr6	56031405	rs112307837	C	T	257.41	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;ClippingRankSum=0.696;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.393;POSITIVE_TRAIN_SITE;QD=23.40;ReadPosRankSum=0.696;SOR=3.258;VQSLOD=5.30;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,9:10:8:285,0,8
-chr6	56033094	rs35471617	G	A	1337.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;ClippingRankSum=-0.876;DB;DP=117;FS=1.690;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=1.143;POSITIVE_TRAIN_SITE;QD=11.43;ReadPosRankSum=1.054;SOR=0.910;VQSLOD=2.31;culprit=DP	GT:AD:DP:GQ:PL	0/1:70,47:117:99:1366,0,2112
-chr6	56037700	rs2397204	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56038131	rs9357892	A	C	266.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.16;SOR=1.609;VQSLOD=6.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:295,21,0
-chr6	56038152	rs1925186	C	G	388.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.093;VQSLOD=6.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:30:417,30,0
-chr6	56038178	rs9357893	G	A	104.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;ClippingRankSum=0.633;DB;DP=11;FS=6.990;MLEAC=1;MLEAF=0.500;MQ=56.09;MQ0=0;MQRankSum=1.447;POSITIVE_TRAIN_SITE;QD=9.52;ReadPosRankSum=0.365;SOR=3.258;VQSLOD=1.97;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,4:10:99:133,0,206
-chr6	56038210	rs77593705	G	C	155.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;ClippingRankSum=-1.268;DB;DP=11;FS=5.441;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.336;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.470;SOR=0.662;VQSLOD=2.59;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,5:10:99:184,0,147
-chr6	56044578	rs2038149	T	C	10645.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=271;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.32;SOR=1.041;VQSLOD=2.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,271:271:99:10674,815,0
-chr6	56045043	rs2038150	C	A	1313.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=7.054;VQSLOD=6.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1342,99,0
-chr6	56045393	rs6933151	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56076639	rs6939465	A	C	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	56076688	rs6939632	C	T	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	56078396	rs6908195	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56080842	rs4126555	A	G	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	56090871	rs3846924	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56094789	rs1925147	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56135778	.	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56141614	rs141389271	G	GT	509.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.917;ClippingRankSum=0.694;DB;DP=108;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=0.858;QD=4.72;ReadPosRankSum=-0.709;SOR=0.467;VQSLOD=3.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,26:60:99:547,0,668
-chr6	56149855	rs9475651	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56149857	rs4715605	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	56160179	rs4432980	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56163121	rs9396195	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56184256	rs4593354	T	C	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	56231275	rs60251615	GT	G	22.73	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:59,6,0
-chr6	56241523	rs6915564	T	G	134.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.51;SOR=3.258;VQSLOD=7.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:162,12,0
-chr6	56271872	rs10456188	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56289250	rs623582	G	A	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	56357668	rs376190394	CA	C	95.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.642;ClippingRankSum=-0.049;DB;DP=93;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=1.135;QD=1.03;ReadPosRankSum=-0.148;SOR=0.156;VQSLOD=4.06;culprit=FS	GT:AD:DP:GQ:PL	0/1:52,15:67:99:133,0,976
-chr6	56365814	rs4283892	A	G	5670.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=169;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.55;SOR=2.647;VQSLOD=4.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,169:169:99:5699,507,0
-chr6	56371698	rs9296848	A	G	6846.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=170;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.83;SOR=7.452;VQSLOD=5.12;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,168:168:99:6875,506,0
-chr6	56373536	rs41271862	C	T	2810.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.287;ClippingRankSum=-0.385;DB;DP=179;FS=1.419;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.394;POSITIVE_TRAIN_SITE;QD=15.70;ReadPosRankSum=1.719;SOR=0.556;VQSLOD=2.22;culprit=DP	GT:AD:DP:GQ:PL	0/1:86,93:179:99:2839,0,2900
-chr6	56374754	rs9296849	C	A	3283.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.38;SOR=6.689;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3312,259,0
-chr6	56380064	rs5876514	CAT	C	739.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=62.94;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.20;SOR=5.892;VQSLOD=6.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,18:18:54:777,54,0
-chr6	56381912	rs4715626	G	A	9981.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.00;AN=2;BaseQRankSum=1.706;ClippingRankSum=-1.538;DB;DP=273;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;MQRankSum=-1.409;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.78;ReadPosRankSum=1.474;SOR=2.272;VQSLOD=-5.700e-03;culprit=FS	GT:AD:DP:GQ:PL	1/1:1,267:268:99:10010,795,0
-chr6	56394173	rs9357922	T	C	2768.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=8.526;VQSLOD=7.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2797,210,0
-chr6	56395051	rs6939305	C	A	2021.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.27;SOR=7.941;VQSLOD=7.06;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2050,157,0
-chr6	56396694	rs34224935	CT	C	39.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.85;SOR=0.693;VQSLOD=7.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	56399731	rs7758054	A	T	964.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.50;SOR=6.518;VQSLOD=5.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,25:25:75:993,75,0
-chr6	56401999	rs4472350	G	A	91.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=9.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	56403072	.	G	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	56410533	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56417282	rs4715630	C	T	12421.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=331;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.31;SOR=1.081;VQSLOD=3.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,331:331:99:12450,995,0
-chr6	56417545	rs4715631	T	C	10049.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=259;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.059;VQSLOD=4.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,259:259:99:10078,779,0
-chr6	56425284	rs2067543	A	G	1201.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.751;ClippingRankSum=0.059;DB;DP=57;FS=3.927;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.652;POSITIVE_TRAIN_SITE;QD=21.08;ReadPosRankSum=0.296;SOR=0.220;VQSLOD=2.01;culprit=QD	GT:AD:DP:GQ:PL	0/1:19,38:57:99:1230,0,587
-chr6	56425497	rs200368513	C	A	36.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.37;SOR=2.303;VQSLOD=6.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:64,6,0
-chr6	56425900	rs1884284	G	A	26.78	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=8.93;ReadPosRankSum=-0.736;SOR=1.179	GT:AD:DP:GQ:PL	0/1:1,2:3:35:55,0,35
-chr6	56425921	rs1884285	T	A	80.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.920;ClippingRankSum=0.684;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=8.97;ReadPosRankSum=0.684;SOR=1.179;VQSLOD=4.63;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:118,0,116
-chr6	56425971	rs1884286	A	G	590.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.542;ClippingRankSum=-0.814;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.374;POSITIVE_TRAIN_SITE;QD=19.69;ReadPosRankSum=-0.330;SOR=1.536;VQSLOD=5.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,20:30:99:619,0,310
-chr6	56426562	rs9357923	G	A	403.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.202;ClippingRankSum=-0.527;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.837;POSITIVE_TRAIN_SITE;QD=17.56;ReadPosRankSum=-0.155;SOR=0.963;VQSLOD=5.73;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,13:23:99:432,0,331
-chr6	56426931	rs9367689	C	T	2689.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.370;ClippingRankSum=0.043;DB;DP=192;FS=4.778;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.486;POSITIVE_TRAIN_SITE;QD=14.01;ReadPosRankSum=2.114;SOR=0.409;VQSLOD=2.13;culprit=DP	GT:AD:DP:GQ:PL	0/1:95,96:191:99:2718,0,3023
-chr6	56427095	rs79573569	C	CTGAGTGTTGAAA	1073.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.359;ClippingRankSum=0.523;DB;DP=57;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.02;MQ0=0;MQRankSum=-4.897;POSITIVE_TRAIN_SITE;QD=18.84;ReadPosRankSum=-1.568;SOR=0.483;VQSLOD=0.980;culprit=FS	GT:AD:DP:GQ:PL	0/1:32,25:57:99:1111,0,1888
-chr6	56437465	rs1014309	T	C	1445.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.090;ClippingRankSum=0.209;DB;DP=89;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=16.24;ReadPosRankSum=1.427;SOR=0.648;VQSLOD=5.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:45,43:88:99:1474,0,1510
-chr6	56437902	rs2144405	C	T	1056.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.383;ClippingRankSum=0.809;DB;DP=66;FS=1.316;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.951;POSITIVE_TRAIN_SITE;QD=16.01;ReadPosRankSum=-1.516;SOR=0.461;VQSLOD=2.55;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:31,35:66:99:1085,0,1085
-chr6	56453346	rs6919941	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56458332	.	T	A	301.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.437;ClippingRankSum=0.441;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=-3.737;QD=10.78;ReadPosRankSum=-1.927;SOR=0.460;VQSLOD=-8.078e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:16,12:28:99:330,0,2663
-chr6	56458334	.	G	A	282.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;ClippingRankSum=0.476;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=-3.134;QD=8.84;ReadPosRankSum=-0.992;SOR=0.260;VQSLOD=0.189;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:21,11:32:99:311,0,3242
-chr6	56458337	.	G	A	260.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.343;ClippingRankSum=-0.083;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.95;MQ0=0;MQRankSum=-3.199;QD=6.86;ReadPosRankSum=-0.878;SOR=0.134;VQSLOD=-4.171e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:28,10:38:99:289,0,3630
-chr6	56458338	.	T	A	215.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=4.133;ClippingRankSum=-0.659;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-3.522;NEGATIVE_TRAIN_SITE;QD=5.53;ReadPosRankSum=-2.300;SOR=0.126;VQSLOD=-2.429e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:29,10:39:99:244,0,3725
-chr6	56458339	.	AGGCT	A	206.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.653;ClippingRankSum=-1.136;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.56;MQ0=0;MQRankSum=-3.349;QD=4.81;ReadPosRankSum=-3.027;SOR=0.100;VQSLOD=-5.999e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:33,10:43:99:244,0,3725
-chr6	56462840	rs9370541	G	A	2994.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.431;ClippingRankSum=-1.553;DB;DP=213;FS=6.435;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=0.686;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.540;SOR=1.216;VQSLOD=2.10;culprit=DP	GT:AD:DP:GQ:PL	0/1:118,95:213:99:3023,0,3656
-chr6	56463410	rs4712138	T	C	5519.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.361;ClippingRankSum=-0.682;DB;DP=398;FS=13.317;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.637;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.87;ReadPosRankSum=2.315;SOR=0.352;VQSLOD=-4.795e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:208,189:397:99:5548,0,6660
-chr6	56466999	rs9382653	T	G	75.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=6.62;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:63:104,0,63
-chr6	56467586	rs11751914	G	A	530.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.043;ClippingRankSum=1.304;DB;DP=35;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.403;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.601;SOR=0.641;VQSLOD=5.46;culprit=FS	GT:AD:DP:GQ:PL	0/1:18,17:35:99:559,0,665
-chr6	56468238	rs9370543	G	A	3348.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=8.795;ClippingRankSum=0.055;DB;DP=200;FS=1.921;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.619;POSITIVE_TRAIN_SITE;QD=16.74;ReadPosRankSum=2.983;SOR=0.871;VQSLOD=2.18;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:102,97:199:99:3377,0,3183
-chr6	56468537	rs9382656	T	C	5633.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=8.003;ClippingRankSum=-2.016;DB;DP=287;FS=2.022;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.379;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.63;ReadPosRankSum=-1.151;SOR=0.827;VQSLOD=0.525;culprit=DP	GT:AD:DP:GQ:PL	0/1:124,162:286:99:5662,0,3728
-chr6	56470551	rs13194995	T	A	4264.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.507;ClippingRankSum=-0.154;DB;DP=311;FS=0.415;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.365;POSITIVE_TRAIN_SITE;QD=13.71;ReadPosRankSum=0.256;SOR=0.662;VQSLOD=1.73;culprit=FS	GT:AD:DP:GQ:PL	0/1:169,141:310:99:4293,0,5525
-chr6	56470690	rs13209548	G	A	4581.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;ClippingRankSum=0.043;DB;DP=298;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-1.592;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=1.757;SOR=0.668;VQSLOD=1.27;culprit=FS	GT:AD:DP:GQ:PL	0/1:151,147:298:99:4610,0,4504
-chr6	56471402	rs9382658	G	A	5089.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.363;ClippingRankSum=0.422;DB;DP=342;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.581;POSITIVE_TRAIN_SITE;QD=14.88;ReadPosRankSum=0.721;SOR=0.676;VQSLOD=1.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:182,158:340:99:5118,0,6087
-chr6	56471995	rs16888055	C	T	2905.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.315;ClippingRankSum=0.444;DB;DP=194;FS=5.194;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=0.379;POSITIVE_TRAIN_SITE;QD=14.98;ReadPosRankSum=1.462;SOR=1.052;VQSLOD=2.30;culprit=DP	GT:AD:DP:GQ:PL	0/1:97,95:192:99:2934,0,3313
-chr6	56476023	rs9370544	G	A	43.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.14;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:27:72,0,27
-chr6	56476182	rs10643818	T	TAAGTA	257.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.783;ClippingRankSum=0.790;DB;DP=31;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=-1.828;POSITIVE_TRAIN_SITE;QD=8.31;ReadPosRankSum=-0.384;SOR=0.132;VQSLOD=5.82;culprit=FS	GT:AD:DP:GQ:PL	0/1:23,8:31:99:295,0,1187
-chr6	56476262	rs7747060	T	C	1532.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.526;ClippingRankSum=-0.045;DB;DP=116;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=-0.777;POSITIVE_TRAIN_SITE;QD=13.21;ReadPosRankSum=-0.453;SOR=0.898;VQSLOD=2.87;culprit=DP	GT:AD:DP:GQ:PL	0/1:67,49:116:99:1561,0,2190
-chr6	56476456	rs9396226	T	A	997.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.112;ClippingRankSum=0.345;DB;DP=87;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.224;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.466;SOR=0.980;VQSLOD=4.80;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,44:78:99:1035,0,1041
-chr6	56482704	rs9396228	A	C	747.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.823;ClippingRankSum=-0.173;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.209;POSITIVE_TRAIN_SITE;QD=10.39;ReadPosRankSum=2.168;SOR=0.735;VQSLOD=4.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:48,24:72:99:776,0,1600
-chr6	56482801	rs6459166	C	G	2911.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.925;ClippingRankSum=0.679;DB;DP=217;FS=5.006;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.577;POSITIVE_TRAIN_SITE;QD=13.42;ReadPosRankSum=1.457;SOR=1.052;VQSLOD=2.17;culprit=DP	GT:AD:DP:GQ:PL	0/1:119,98:217:99:2940,0,3555
-chr6	56484758	rs2230862	C	T	1769.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.905;ClippingRankSum=1.335;DB;DP=147;FS=6.412;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=1.822;POSITIVE_TRAIN_SITE;QD=12.04;ReadPosRankSum=0.721;SOR=0.357;VQSLOD=1.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:86,61:147:99:1798,0,2992
-chr6	56496649	rs10456737	A	C	1638.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.101;ClippingRankSum=-1.291;DB;DP=80;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.160;POSITIVE_TRAIN_SITE;QD=20.48;ReadPosRankSum=0.671;SOR=0.763;VQSLOD=5.14;culprit=FS	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1667,0,816
-chr6	56507135	rs1024195	T	C	1136.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.677;ClippingRankSum=0.952;DB;DP=56;FS=1.927;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=20.30;ReadPosRankSum=-0.108;SOR=1.511;VQSLOD=2.71;culprit=QD	GT:AD:DP:GQ:PL	0/1:24,32:56:99:1165,0,749
-chr6	56701620	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.50;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56736574	.	TA	T	49.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.817;ClippingRankSum=1.184;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=0.531;QD=1.91;ReadPosRankSum=1.312;SOR=0.602;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,9:19:87:87,0,131
-chr6	56818706	rs986245	T	C	816.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.03;SOR=2.925;VQSLOD=6.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,24:24:72:845,72,0
-chr6	56827628	rs9349841	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56846334	rs9396247	A	G	342.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=4.615;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,9:9:27:371,27,0
-chr6	56873069	rs6925819	T	C	1050.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.57;SOR=3.912;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1079,90,0
-chr6	56893978	rs58747062	TC	T	28.71	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.35;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:65,6,0
-chr6	56894940	rs34180205	CG	C	106	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.20;SOR=3.258;VQSLOD=5.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:143,12,0
-chr6	56900699	rs3996934	C	T	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	56917538	rs6926980	G	A	2244.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.357;ClippingRankSum=0.056;DB;DP=147;FS=7.253;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.138;POSITIVE_TRAIN_SITE;QD=15.27;ReadPosRankSum=2.288;SOR=0.714;VQSLOD=2.13;culprit=FS	GT:AD:DP:GQ:PL	0/1:74,73:147:99:2273,0,2345
-chr6	56919443	rs61740375	A	G	752.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.392;ClippingRankSum=-0.128;DB;DP=52;FS=10.283;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.769;POSITIVE_TRAIN_SITE;QD=14.48;ReadPosRankSum=1.044;SOR=0.065;VQSLOD=1.36;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,25:52:99:781,0,941
-chr6	56963708	rs9367711	T	G	789.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.396;ClippingRankSum=-0.682;DB;DP=55;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.513;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.295;SOR=0.729;VQSLOD=5.51;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,28:55:99:818,0,939
-chr6	56994594	rs7758913	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	56998023	rs3757296	A	G	2007.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.613;ClippingRankSum=-0.822;DB;DP=133;FS=2.401;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.518;POSITIVE_TRAIN_SITE;QD=15.10;ReadPosRankSum=-1.605;SOR=0.503;VQSLOD=2.33;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:64,67:131:99:2036,0,2080
-chr6	57006391	rs2273919	C	T	310.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.573;ClippingRankSum=-0.380;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=1.356;POSITIVE_TRAIN_SITE;QD=19.42;ReadPosRankSum=2.007;SOR=1.244;VQSLOD=5.45;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,10:16:99:339,0,197
-chr6	57006933	rs2273921	T	C	1686.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.719;ClippingRankSum=0.791;DB;DP=136;FS=8.160;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.554;POSITIVE_TRAIN_SITE;QD=12.40;ReadPosRankSum=0.949;SOR=1.463;VQSLOD=2.01;culprit=FS	GT:AD:DP:GQ:PL	0/1:76,60:136:99:1715,0,2402
-chr6	57012930	rs3734738	C	T	2118.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.567;ClippingRankSum=-0.086;DB;DP=161;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.460;POSITIVE_TRAIN_SITE;QD=13.16;ReadPosRankSum=-1.077;SOR=0.558;VQSLOD=2.37;culprit=DP	GT:AD:DP:GQ:PL	0/1:87,74:161:99:2147,0,2812
-chr6	57048458	rs9885757	C	T	476.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.695;ClippingRankSum=-0.057;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.057;POSITIVE_TRAIN_SITE;QD=14.90;ReadPosRankSum=0.019;SOR=0.693;VQSLOD=5.92;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,16:32:99:505,0,556
-chr6	57055354	rs1040461	C	T	2987.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.147;ClippingRankSum=-2.243;DB;DP=178;FS=1.900;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.750;POSITIVE_TRAIN_SITE;QD=16.79;ReadPosRankSum=0.605;SOR=0.855;VQSLOD=2.11;culprit=DP	GT:AD:DP:GQ:PL	0/1:81,97:178:99:3016,0,2448
-chr6	57059820	rs9357940	T	G	252.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.739;ClippingRankSum=0.627;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.739;POSITIVE_TRAIN_SITE;QD=18.05;ReadPosRankSum=0.715;SOR=0.976;VQSLOD=6.00;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,8:14:99:281,0,187
-chr6	57074911	rs9357941	G	A	404.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.359;ClippingRankSum=-0.103;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.462;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=-1.538;SOR=0.693;VQSLOD=5.41;culprit=FS	GT:AD:DP:GQ:PL	0/1:13,13:26:99:433,0,497
-chr6	57097549	rs223304	T	C	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57106426	rs223289	T	G	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	57163494	rs7770252	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57182297	rs1019210	C	T	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=6.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	57183869	.	A	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	57188889	rs79594432	A	T	460.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;ClippingRankSum=0.415;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.756;POSITIVE_TRAIN_SITE;QD=17.07;ReadPosRankSum=-0.512;SOR=0.922;VQSLOD=5.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,15:27:99:489,0,381
-chr6	57191021	rs11381745	A	AG	1131.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.10;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.02;SOR=7.054;VQSLOD=6.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1169,99,0
-chr6	57209749	rs9475860	C	T	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;SOR=2.303;VQSLOD=6.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	57209802	rs1024706	T	C	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	57209865	rs5876534	GA	G	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57209889	rs1024705	G	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.52;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57213782	rs7772897	A	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57213785	rs7755104	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57226182	rs17705499	C	T	51.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=12.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:29:80,0,29
-chr6	57228571	rs12193422	G	A	48.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.15;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:29:77,0,29
-chr6	57228598	rs6911124	A	G	51.79	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;QD=12.95;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.09;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:23:80,0,23
-chr6	57228685	rs6911177	A	G	123.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;ClippingRankSum=-0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.720;QD=20.63;ReadPosRankSum=-0.720;SOR=0.693;VQSLOD=4.71;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:99:152,0,126
-chr6	57228704	rs6934266	T	G	46.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;QD=9.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=4.40;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,2:5:75:75,0,154
-chr6	57228809	rs6911507	A	C	50.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.92;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:79,0,32
-chr6	57231331	rs2079934	G	T	32.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.36;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:61,0,32
-chr6	57231352	rs2397239	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57231354	rs2397240	A	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57232345	rs12200857	G	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:28:40,0,28
-chr6	57232902	rs62417969	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57234078	rs9464454	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57243144	rs12201524	G	A	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=4.21;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,154
-chr6	57243154	rs12201527	G	A	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=4.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,154
-chr6	57244492	rs7759919	T	C	24.78	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.572;ClippingRankSum=-1.067;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.572;QD=3.10;ReadPosRankSum=-1.067;SOR=0.169	GT:AD:DP:GQ:PL	0/1:6,2:8:53:53,0,209
-chr6	57244509	rs5011405	T	G	34.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.589;ClippingRankSum=1.589;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=4.35;ReadPosRankSum=-0.572;SOR=0.169;VQSLOD=5.46;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,2:8:63:63,0,213
-chr6	57244672	rs5011404	G	A	2178.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.306;ClippingRankSum=2.205;DB;DP=136;FS=2.003;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.847;POSITIVE_TRAIN_SITE;QD=16.02;ReadPosRankSum=0.446;SOR=1.017;VQSLOD=2.92;culprit=DP	GT:AD:DP:GQ:PL	0/1:66,70:136:99:2207,0,2213
-chr6	57244780	rs5011403	G	A	3287.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.453;ClippingRankSum=0.408;DB;DP=235;FS=0.510;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.808;QD=13.99;ReadPosRankSum=0.963;SOR=0.634;VQSLOD=0.424;culprit=FS	GT:AD:DP:GQ:PL	0/1:123,112:235:99:3316,0,3653
-chr6	57244830	rs5011402	T	A	2187.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.318;ClippingRankSum=1.365;DB;DP=134;FS=4.341;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-1.290;QD=16.33;ReadPosRankSum=0.292;SOR=0.162;VQSLOD=0.141;culprit=DP	GT:AD:DP:GQ:PL	0/1:64,70:134:99:2216,0,2120
-chr6	57244893	rs5011401	T	C	609.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.502;ClippingRankSum=-0.431;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.260;POSITIVE_TRAIN_SITE;QD=17.93;ReadPosRankSum=2.018;SOR=0.811;VQSLOD=4.32;culprit=FS	GT:AD:DP:GQ:PL	0/1:16,18:34:99:638,0,509
-chr6	57244979	rs5011400	G	A	91.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.54;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:99:120,0,137
-chr6	57244982	rs5011399	C	T	91.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.34;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:99:120,0,137
-chr6	57246581	rs62415468	T	A	183.85	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;ClippingRankSum=-0.742;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=-0.742;QD=26.26;ReadPosRankSum=-0.742;SOR=2.584;VQSLOD=3.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,6:7:17:212,0,17
-chr6	57246614	rs62415469	T	C	379.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.371;ClippingRankSum=-2.285;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.718;QD=25.32;ReadPosRankSum=-1.371;SOR=1.911;VQSLOD=3.76;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,11:15:99:408,0,118
-chr6	57246638	rs6913328	C	T	668.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.214;ClippingRankSum=-1.226;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.603;QD=20.90;ReadPosRankSum=1.654;SOR=1.284;VQSLOD=3.38;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,20:32:99:697,0,376
-chr6	57246708	rs6913779	G	T	1443.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.155;ClippingRankSum=0.128;DB;DP=141;FS=4.590;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-1.089;QD=10.24;ReadPosRankSum=-0.829;SOR=0.067;VQSLOD=-7.831e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:92,49:141:99:1472,0,3506
-chr6	57246773	rs113849959	T	TAGG	4992.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;ClippingRankSum=0.124;DB;DP=309;FS=5.829;MLEAC=1;MLEAF=0.500;MQ=57.08;MQ0=0;MQRankSum=-3.483;NEGATIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=1.260;SOR=1.145;VQSLOD=-2.405e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:174,127:301:99:5030,0,7083
-chr6	57246785	rs62415470	A	C	5492.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=8.898;ClippingRankSum=-0.346;DB;DP=349;FS=1.043;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=0;MQRankSum=-1.730;QD=15.74;ReadPosRankSum=1.758;SOR=0.781;VQSLOD=-7.042e-01;culprit=DP	GT:AD:DP:GQ:PL	0/1:201,148:349:99:5521,0,7683
-chr6	57246815	rs6936571	T	C	5593.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=6.746;ClippingRankSum=-1.594;DB;DP=416;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-1.167;NEGATIVE_TRAIN_SITE;QD=13.45;ReadPosRankSum=-1.267;SOR=0.707;VQSLOD=-1.509e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:229,187:416:99:5622,0,7181
-chr6	57246878	rs61753604	T	C	1938.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.885;ClippingRankSum=1.162;DB;DP=444;FS=0.650;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-1.757;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=4.37;ReadPosRankSum=0.012;SOR=0.802;VQSLOD=-1.920e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:350,94:444:99:1967,0,13279
-chr6	57246884	rs6913546	A	G	7065.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=3.408;ClippingRankSum=-0.389;DB;DP=440;FS=0.524;MLEAC=1;MLEAF=0.500;MQ=58.70;MQ0=0;MQRankSum=-2.305;NEGATIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-1.094;SOR=0.630;VQSLOD=-2.286e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:227,212:439:99:7094,0,7015
-chr6	57246969	rs4256440	G	A	4783.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.872;ClippingRankSum=0.620;DB;DP=347;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=-0.808;QD=13.79;ReadPosRankSum=-0.427;SOR=0.712;VQSLOD=-4.860e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:182,163:345:99:4812,0,6048
-chr6	57246982	rs4585567	G	T	4000.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.751;ClippingRankSum=0.330;DB;DP=315;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-0.546;QD=12.70;ReadPosRankSum=-0.935;SOR=0.712;VQSLOD=-5.530e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:174,139:313:99:4029,0,5824
-chr6	57247022	rs4382263	C	T	3135.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.094;ClippingRankSum=-0.825;DB;DP=206;FS=9.797;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=0.277;QD=15.22;ReadPosRankSum=0.532;SOR=1.811;VQSLOD=-7.670e-02;culprit=FS	GT:AD:DP:GQ:PL	0/1:108,98:206:99:3164,0,3645
-chr6	57247093	rs4499918	A	T	892.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.606;ClippingRankSum=0.186;DB;DP=63;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.52;MQ0=0;MQRankSum=0.131;QD=14.17;ReadPosRankSum=-0.517;SOR=0.551;VQSLOD=2.59;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,29:63:99:921,0,1186
-chr6	57247108	rs4507595	G	A	668.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.825;ClippingRankSum=0.298;DB;DP=53;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-0.262;QD=12.62;ReadPosRankSum=0.406;SOR=0.416;VQSLOD=3.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:31,22:53:99:697,0,1110
-chr6	57247121	rs4310040	T	C	577.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.370;ClippingRankSum=-1.834;DB;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.849;QD=13.44;ReadPosRankSum=-0.382;SOR=0.428;VQSLOD=3.58;culprit=FS	GT:AD:DP:GQ:PL	0/1:25,18:43:99:606,0,856
-chr6	57259789	rs149275162	C	A	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57259808	rs117189504	A	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57259820	rs114240725	C	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57260463	rs9475913	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57262992	rs2894847	A	G	11.83	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.83;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:38,3,0
-chr6	57263008	rs72871660	G	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57284914	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57296209	rs78775831	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=9.30;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57296216	rs80242777	C	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=9.30;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57296249	rs72873542	C	G	16.63	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=8.31;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	57303056	rs62401712	T	C	40.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=13.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.28;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:29:69,0,29
-chr6	57303102	rs62401713	A	G	15.43	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=5.14;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:1:41,0,1
-chr6	57307716	rs60930046	T	C	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57307784	rs60600423	C	G	73.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=24.43;SOR=1.179;VQSLOD=5.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:101,9,0
-chr6	57309839	rs5003056	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57310132	rs73750278	C	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57310138	rs73750279	C	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57310284	rs9464491	A	G	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=5.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57310326	rs73750281	T	G	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57310334	rs73750282	T	C	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.59;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57315082	rs12204748	G	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57325633	rs4715697	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57326248	rs2145339	A	G	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=7.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	57326568	rs9464502	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57330320	rs9382742	T	C	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57336157	rs9476010	G	A	30.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.380;QD=5.13;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=3.01;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,2:6:59:59,0,154
-chr6	57336243	rs9476012	G	A	39.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=9.94;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=3.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:68:68,0,78
-chr6	57336279	rs9476013	C	G	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=4.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,78
-chr6	57336284	rs9476014	A	G	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=12.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.33;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,78
-chr6	57336340	rs1570072	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57342040	rs13219968	T	C	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	57345089	rs5024768	G	C	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57347208	.	T	TG	21.73	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0
-chr6	57347800	rs34877937	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57347818	rs35142105	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57348150	rs34523439	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57348155	rs35239416	A	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57348440	rs34411188	A	G	50.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=1.11;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:1,2:3:28:79,0,28
-chr6	57348501	rs35975405	T	C	71.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.34;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	57348518	rs71221642	A	G	71.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	57348534	rs34153534	G	A	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.69;SOR=1.179;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57348538	rs34509185	T	G	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.33;SOR=1.179;VQSLOD=6.95;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57349040	rs9476023	T	C	93.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	57349257	rs9476024	C	T	16.63	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.63;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	57349280	rs12198778	A	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=7.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	57349405	rs9476025	A	G	17.61	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.61;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:44,3,0
-chr6	57349426	rs9476026	C	T	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57349572	rs6929331	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57349576	rs4715714	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57350134	rs9367752	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57353249	rs4715715	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57355968	rs35947597	T	A	102.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=7.02;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	57355975	.	C	A	102.28	PASS	AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=5.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	57355995	rs36115431	G	A	102.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=6.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:130,9,0
-chr6	57356611	rs9476033	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57358196	rs36181256	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57358870	rs4991170	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57358888	rs5876577	T	TC	37.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.85;SOR=0.693;VQSLOD=7.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	57362013	rs62399733	T	C	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:31:40,0,31
-chr6	57362029	rs73752496	A	G	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.73;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:74:81,0,74
-chr6	57362030	rs72877164	C	T	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.56;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:74:81,0,74
-chr6	57362057	rs12526351	G	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:36:40,0,36
-chr6	57364996	rs73755520	C	T	32.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=3.31;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,2:4:61:61,0,76
-chr6	57365151	rs5025370	T	C	47.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=5.00;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:35:76,0,35
-chr6	57366534	rs4715718	G	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.68;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57366536	rs4715719	A	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57368219	rs62400883	G	A	36.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=12.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.12;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:30:65,0,30
-chr6	57369510	rs62400894	A	G	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57371913	rs59066164	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371916	rs75944038	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371926	rs10949092	A	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371931	rs74978393	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57371939	rs10949093	G	A	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.87;SOR=0.693;VQSLOD=7.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	57371962	rs10949094	T	A	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=6.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	57372104	rs2024986	T	C	162.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.512;ClippingRankSum=0.514;DB;DP=25;FS=5.528;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.091;QD=6.51;ReadPosRankSum=0.212;SOR=0.033;VQSLOD=0.457;culprit=QD	GT:AD:DP:GQ:PL	0/1:18,7:25:99:191,0,669
-chr6	57372116	rs9382768	T	C	752.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;ClippingRankSum=0.589;DB;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.589;QD=25.96;ReadPosRankSum=-0.778;SOR=1.688;VQSLOD=2.67;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,20:29:99:781,0,276
-chr6	57372126	rs9396314	C	G	253.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.170;ClippingRankSum=-1.868;DB;DP=35;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.510;POSITIVE_TRAIN_SITE;QD=7.25;ReadPosRankSum=0.698;SOR=0.129;VQSLOD=4.41;culprit=QD	GT:AD:DP:GQ:PL	0/1:26,9:35:99:282,0,1018
-chr6	57372199	rs9382769	T	C	3132.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=8.094;ClippingRankSum=0.441;DB;DP=131;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.586;QD=23.91;ReadPosRankSum=-0.007;SOR=1.470;VQSLOD=1.39;culprit=FS	GT:AD:DP:GQ:PL	0/1:46,85:131:99:3161,0,1398
-chr6	57372361	rs9382770	C	A	10336.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.385;ClippingRankSum=-0.913;DB;DP=437;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=1.326;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.567;SOR=0.720;VQSLOD=-2.151e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:149,287:436:99:10365,0,4146
-chr6	57372365	rs9396315	A	G	3727.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.398;ClippingRankSum=-0.329;DB;DP=443;FS=0.613;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=3.315;NEGATIVE_TRAIN_SITE;QD=8.41;ReadPosRankSum=0.164;SOR=0.610;VQSLOD=-3.453e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:298,144:442:99:3756,0,10951
-chr6	57372374	rs68090917	CT	C	3672.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.835;ClippingRankSum=0.028;DB;DP=420;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=0.217;POSITIVE_TRAIN_SITE;QD=8.74;ReadPosRankSum=0.275;SOR=0.674;VQSLOD=-1.464e-01;culprit=DP	GT:AD:DP:GQ:PL	0/1:274,132:406:99:3710,0,8968
-chr6	57372436	rs9382771	G	C	4364.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=4.675;ClippingRankSum=0.150;DB;DP=201;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-2.890;NEGATIVE_TRAIN_SITE;QD=21.72;ReadPosRankSum=0.305;SOR=1.373;VQSLOD=-1.610e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:74,127:201:99:4393,0,2326
-chr6	57372437	rs79221898	C	T	2323.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.294;ClippingRankSum=-0.543;DB;DP=202;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=0.030;QD=11.50;ReadPosRankSum=0.294;SOR=0.345;VQSLOD=0.165;culprit=FS	GT:AD:DP:GQ:PL	0/1:123,79:202:99:2352,0,4259
-chr6	57372456	rs35141035	AT	A	952.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.481;ClippingRankSum=0.386;DB;DP=149;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=0;MQRankSum=-1.225;POSITIVE_TRAIN_SITE;QD=6.39;ReadPosRankSum=0.325;SOR=0.544;VQSLOD=3.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:65,50:115:99:990,0,1228
-chr6	57372480	rs79601039	A	G	1090.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.462;ClippingRankSum=-0.042;DB;DP=82;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=0.276;QD=13.30;ReadPosRankSum=1.108;SOR=0.482;VQSLOD=3.82;culprit=FS	GT:AD:DP:GQ:PL	0/1:46,36:82:99:1119,0,1889
-chr6	57372502	rs9349872	G	A	894.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.559;ClippingRankSum=-0.640;DB;DP=44;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=0;MQRankSum=-3.815;QD=20.34;ReadPosRankSum=-0.166;SOR=0.990;VQSLOD=0.816;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:19,25:44:99:923,0,664
-chr6	57372510	rs77697887	T	G	453.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.557;ClippingRankSum=0.318;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-3.102;QD=11.94;ReadPosRankSum=-1.226;SOR=0.307;VQSLOD=0.504;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:24,14:38:99:482,0,966
-chr6	57372514	rs77868044	T	C	425.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.126;ClippingRankSum=0.397;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.03;MQ0=0;MQRankSum=-1.547;QD=13.31;ReadPosRankSum=-1.389;SOR=0.260;VQSLOD=2.80;culprit=FS	GT:AD:DP:GQ:PL	0/1:21,11:32:99:454,0,927
-chr6	57372523	rs10706124	TG	T	235.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;ClippingRankSum=0.381;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.16;MQ0=0;MQRankSum=-3.433;POSITIVE_TRAIN_SITE;QD=8.42;ReadPosRankSum=1.704;SOR=0.169;VQSLOD=2.42;culprit=FS	GT:AD:DP:GQ:PL	0/1:20,8:28:99:273,0,858
-chr6	57372526	rs10635932	C	CTTTA	238.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.250;ClippingRankSum=1.472;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.24;MQ0=0;MQRankSum=-3.139;POSITIVE_TRAIN_SITE;QD=9.18;ReadPosRankSum=1.694;SOR=0.202;VQSLOD=2.74;culprit=FS	GT:AD:DP:GQ:PL	0/1:18,8:26:99:276,0,816
-chr6	57372583	rs9367754	C	T	93.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=-0.937;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-0.937;QD=13.40;ReadPosRankSum=0.000;SOR=0.941;VQSLOD=4.53;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:99:122,0,108
-chr6	57372611	rs9382772	C	T	32.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=3.39;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,2:4:61:61,0,77
-chr6	57374364	rs75332238	C	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	57379671	rs4573085	C	G	43.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;QD=10.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=4.49;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:24:72,0,24
-chr6	57379715	rs2894901	T	G	98.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=24.51;SOR=1.609;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:126,12,0
-chr6	57379745	rs9476056	G	A	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57384745	rs75634578	T	C	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	57385801	rs4715735	A	G	39.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=19.87;SOR=0.693;VQSLOD=6.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-chr6	57386904	rs149764231	GAGA	G	43.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=2.50;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57389299	rs375498702	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57390094	rs12203268	T	C	12.06	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:25:40,0,25
-chr6	57390107	rs200901455	CATCTGTT	C	40.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=10.18;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=5.20;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,78
-chr6	57390124	rs56102916	G	C	111.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=27.76;SOR=0.693;VQSLOD=5.73;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:139,12,0
-chr6	57390134	rs75555855	C	T	26.78	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=6.69;ReadPosRankSum=1.026;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:55:55,0,78
-chr6	57390168	rs78919924	C	T	29.78	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.804;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:27:58,0,27
-chr6	57392874	rs927195	C	T	110.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.720;QD=18.46;ReadPosRankSum=0.000;SOR=0.368;VQSLOD=4.73;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:61:139,0,61
-chr6	57392913	rs927194	T	C	103.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=-1.638;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.368;POSITIVE_TRAIN_SITE;QD=12.97;ReadPosRankSum=-0.922;SOR=0.693;VQSLOD=6.21;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:132,0,222
-chr6	57392921	rs62398963	T	A	88.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.312;ClippingRankSum=-1.157;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.231;QD=6.83;ReadPosRankSum=-0.386;SOR=0.223;VQSLOD=3.71;culprit=QD	GT:AD:DP:GQ:PL	0/1:9,4:13:99:117,0,346
-chr6	57392963	rs927193	T	C	531.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;ClippingRankSum=-0.110;DB;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.680;QD=18.34;ReadPosRankSum=-0.811;SOR=0.906;VQSLOD=3.89;culprit=FS	GT:AD:DP:GQ:PL	0/1:13,16:29:99:560,0,435
-chr6	57393029	rs77090024	T	A	813.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=3.045;ClippingRankSum=0.061;DB;DP=76;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-4.889;NEGATIVE_TRAIN_SITE;QD=10.71;ReadPosRankSum=2.576;SOR=0.201;VQSLOD=-3.073e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:52,24:76:99:842,0,2229
-chr6	57393034	rs75127850	G	T	1008.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.248;ClippingRankSum=0.023;DB;DP=86;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.50;MQ0=0;MQRankSum=-5.580;NEGATIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=1.286;SOR=0.216;VQSLOD=-3.258e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:58,28:86:99:1037,0,2424
-chr6	57393040	rs74756458	A	T	1158.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.499;ClippingRankSum=-1.753;DB;DP=96;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.21;MQ0=0;MQRankSum=-5.165;NEGATIVE_TRAIN_SITE;QD=12.07;ReadPosRankSum=1.667;SOR=0.229;VQSLOD=-3.001e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:64,32:96:99:1187,0,2672
-chr6	57393054	rs75725892	G	A	1341.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=8.421;ClippingRankSum=0.555;DB;DP=120;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.42;MQ0=0;MQRankSum=-4.298;NEGATIVE_TRAIN_SITE;QD=11.18;ReadPosRankSum=1.283;SOR=1.179;VQSLOD=-2.209e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:81,39:120:99:1370,0,3620
-chr6	57393074	rs73752376	A	G	1772.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=7.296;ClippingRankSum=0.236;DB;DP=171;FS=3.973;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-2.664;NEGATIVE_TRAIN_SITE;QD=10.37;ReadPosRankSum=0.650;SOR=1.329;VQSLOD=-1.602e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:121,50:171:99:1801,0,5032
-chr6	57393092	rs73752377	T	A	2197.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;ClippingRankSum=0.412;DB;DP=234;FS=2.430;MLEAC=1;MLEAF=0.500;MQ=56.70;MQ0=0;MQRankSum=-2.781;NEGATIVE_TRAIN_SITE;QD=9.39;ReadPosRankSum=-0.722;SOR=0.915;VQSLOD=-1.964e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:164,70:234:99:2226,0,6218
-chr6	57393125	rs927192	A	G	7635.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=5.292;ClippingRankSum=-0.772;DB;DP=356;FS=5.930;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=0.055;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.45;ReadPosRankSum=-0.840;SOR=0.430;VQSLOD=-2.175e-01;culprit=DP	GT:AD:DP:GQ:PL	0/1:129,227:356:99:7664,0,3693
-chr6	57393160	rs76686926	G	A	2805.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.132;ClippingRankSum=0.139;DB;DP=395;FS=1.817;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-1.496;NEGATIVE_TRAIN_SITE;QD=7.10;ReadPosRankSum=0.029;SOR=0.592;VQSLOD=-2.787e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:278,117:395:99:2834,0,8784
-chr6	57393199	rs2397502	C	A	3769.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.119;ClippingRankSum=1.716;DB;DP=344;FS=1.419;MLEAC=1;MLEAF=0.500;MQ=58.31;MQ0=0;MQRankSum=2.244;NEGATIVE_TRAIN_SITE;QD=10.96;ReadPosRankSum=0.093;SOR=0.606;VQSLOD=-1.342e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:226,118:344:99:3798,0,8416
-chr6	57393216	rs2397503	G	T	6455.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.047;ClippingRankSum=0.677;DB;DP=273;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=-1.274;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.802;SOR=0.672;VQSLOD=-1.677e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:112,161:273:99:6484,0,4010
-chr6	57393222	rs111989160	A	G	2124.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=6.075;ClippingRankSum=0.447;DB;DP=254;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-0.081;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=1.798;SOR=0.705;VQSLOD=-1.470e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:191,63:254:99:2153,0,7932
-chr6	57393228	rs112156516	G	A	2056.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=7.272;ClippingRankSum=-0.141;DB;DP=242;FS=2.168;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=0.518;NEGATIVE_TRAIN_SITE;QD=8.50;ReadPosRankSum=2.889;SOR=1.002;VQSLOD=-1.477e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:182,60:242:99:2085,0,7456
-chr6	57393278	rs75909609	T	C	978.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=7.163;ClippingRankSum=1.948;DB;DP=126;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=0.294;QD=7.77;ReadPosRankSum=0.566;SOR=0.428;VQSLOD=1.81;culprit=QD	GT:AD:DP:GQ:PL	0/1:93,33:126:99:1007,0,3194
-chr6	57393323	rs12198995	T	C	122.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.995;ClippingRankSum=-0.894;DB;DP=63;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-1.012;QD=1.95;ReadPosRankSum=0.953;SOR=0.033;VQSLOD=0.768;culprit=QD	GT:AD:DP:GQ:PL	0/1:54,9:63:99:151,0,2049
-chr6	57393329	rs76564922	G	T	491.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.488;ClippingRankSum=-0.148;DB;DP=58;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.67;MQ0=0;MQRankSum=1.018;QD=8.48;ReadPosRankSum=0.478;SOR=0.145;VQSLOD=3.43;culprit=QD	GT:AD:DP:GQ:PL	0/1:42,16:58:99:520,0,1666
-chr6	57393337	rs200714656	T	TA	779.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.011;ClippingRankSum=0.247;DB;DP=47;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=16.59;ReadPosRankSum=-0.957;SOR=0.446;VQSLOD=5.50;culprit=FS	GT:AD:DP:GQ:PL	0/1:27,20:47:99:817,0,1052
-chr6	57393338	rs2397504	T	A	1418.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.401;ClippingRankSum=0.911;DB;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-1.809;NEGATIVE_TRAIN_SITE;QD=31.53;ReadPosRankSum=-1.578;SOR=2.059;VQSLOD=-2.208e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,33:45:99:1447,0,396
-chr6	57393350	rs2397505	G	A	577.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.397;ClippingRankSum=-0.510;DB;DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=0;MQRankSum=-2.800;QD=15.62;ReadPosRankSum=-1.686;SOR=0.395;VQSLOD=1.10;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:22,15:37:99:606,0,861
-chr6	57393407	rs374979361	C	T	67.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.683;ClippingRankSum=-0.573;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.248;QD=7.53;ReadPosRankSum=-0.248;SOR=0.283;VQSLOD=4.48;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,3:9:96:96,0,194
-chr6	57393519	rs62398965	A	G	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.50;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57393716	rs2397508	G	A	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	57394939	rs11963080	C	T	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57395058	rs12202626	T	C	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57395077	rs12195527	C	G	61.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.87;SOR=2.303;VQSLOD=7.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:89,6,0
-chr6	57395396	rs74519885	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57396165	rs6924765	G	A	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.82;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:78:81,0,78
-chr6	57396173	rs79246915	G	T	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=4.76;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:78:81,0,78
-chr6	57397866	rs57276498	T	TA	68.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=0.000;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.82;MQ0=0;MQRankSum=-0.720;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.720;SOR=1.329;VQSLOD=5.96;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:38:106,0,38
-chr6	57397944	rs7770986	A	G	201.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.659;ClippingRankSum=-0.183;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=0;MQRankSum=0.183;QD=5.93;ReadPosRankSum=-0.386;SOR=0.392;VQSLOD=2.50;culprit=QD	GT:AD:DP:GQ:PL	0/1:26,8:34:99:230,0,866
-chr6	57397982	rs7771127	C	A	876.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.945;ClippingRankSum=-0.215;DB;DP=57;FS=3.087;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-1.269;QD=15.38;ReadPosRankSum=0.567;SOR=0.197;VQSLOD=1.24;culprit=FS	GT:AD:DP:GQ:PL	0/1:29,28:57:99:905,0,992
-chr6	57398008	rs7771257	C	T	1863.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.114;ClippingRankSum=-0.432;DB;DP=91;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=-1.126;QD=20.48;ReadPosRankSum=-0.093;SOR=0.232;VQSLOD=3.03;culprit=FS	GT:AD:DP:GQ:PL	0/1:44,46:90:99:1892,0,1700
-chr6	57398009	rs7771114	A	G	1863.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.944;ClippingRankSum=0.703;DB;DP=92;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.26;MQ0=0;MQRankSum=-3.030;POSITIVE_TRAIN_SITE;QD=20.26;ReadPosRankSum=-0.203;SOR=0.241;VQSLOD=3.10;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:44,47:91:99:1892,0,1700
-chr6	57398028	rs67286646	TG	T	832.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.812;ClippingRankSum=-0.912;DB;DP=148;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.11;MQ0=0;MQRankSum=0.437;POSITIVE_TRAIN_SITE;QD=5.63;ReadPosRankSum=-0.426;SOR=0.853;VQSLOD=3.92;culprit=FS	GT:AD:DP:GQ:PL	0/1:107,40:147:99:870,0,4153
-chr6	57398047	rs76081480	A	C	1782.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=7.353;ClippingRankSum=-0.762;DB;DP=191;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.74;MQ0=0;MQRankSum=-2.177;NEGATIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.084;SOR=0.701;VQSLOD=-1.736e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:127,63:190:99:1811,0,4583
-chr6	57398058	rs7771283	C	G	1588.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.421;ClippingRankSum=0.238;DB;DP=230;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=1.141;NEGATIVE_TRAIN_SITE;QD=6.91;ReadPosRankSum=-1.687;SOR=0.435;VQSLOD=-2.531e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:168,61:229:99:1617,0,5971
-chr6	57398081	rs7753294	T	G	5599.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=8.745;ClippingRankSum=0.077;DB;DP=263;FS=27.103;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-4.145;NEGATIVE_TRAIN_SITE;QD=21.29;ReadPosRankSum=2.243;SOR=3.663;VQSLOD=-1.976e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:103,159:262:99:5628,0,3075
-chr6	57398117	rs139574925	T	TA	2948.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.101;ClippingRankSum=1.493;DB;DP=361;FS=2.214;MLEAC=1;MLEAF=0.500;MQ=54.59;MQ0=0;MQRankSum=-1.420;NEGATIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=-1.614;SOR=0.901;VQSLOD=-2.236e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:262,99:361:99:2986,0,10807
-chr6	57398118	rs147643173	G	T	2951.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.611;ClippingRankSum=0.472;DB;DP=366;FS=1.357;MLEAC=1;MLEAF=0.500;MQ=54.39;MQ0=0;MQRankSum=-1.610;NEGATIVE_TRAIN_SITE;QD=8.06;ReadPosRankSum=-1.741;SOR=0.841;VQSLOD=-2.741e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:265,101:366:99:2980,0,10921
-chr6	57398154	rs80081867	T	C	9900.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.712;ClippingRankSum=-1.351;DB;DP=417;FS=3.795;MLEAC=1;MLEAF=0.500;MQ=52.44;MQ0=0;MQRankSum=-5.322;NEGATIVE_TRAIN_SITE;QD=23.74;ReadPosRankSum=0.785;SOR=1.039;VQSLOD=-2.613e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:170,247:417:99:9929,0,6569
-chr6	57398157	rs9476080	A	G	10031.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=11.939;ClippingRankSum=-0.670;DB;DP=420;FS=5.630;MLEAC=1;MLEAF=0.500;MQ=52.56;MQ0=0;MQRankSum=-6.161;NEGATIVE_TRAIN_SITE;QD=23.89;ReadPosRankSum=1.335;SOR=1.089;VQSLOD=-2.877e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:174,246:420:99:10060,0,6871
-chr6	57398163	rs9476081	A	G	9691.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.386;ClippingRankSum=-0.317;DB;DP=428;FS=7.782;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=-7.057;NEGATIVE_TRAIN_SITE;QD=22.64;ReadPosRankSum=2.150;SOR=1.207;VQSLOD=-3.250e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:182,246:428:99:9720,0,6877
-chr6	57398186	rs147954160	G	GA	3146.73	VQSRTrancheINDEL99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=1.394;ClippingRankSum=0.081;DB;DP=466;FS=0.612;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=0;MQRankSum=-5.529;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=6.75;ReadPosRankSum=-0.584;SOR=0.648;VQSLOD=-3.838e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:331,119:450:99:3184,0,13464
-chr6	57398201	rs62398997	T	C	9311.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=1.718;ClippingRankSum=0.323;DB;DP=477;FS=1.130;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=0;MQRankSum=-2.722;NEGATIVE_TRAIN_SITE;QD=19.52;ReadPosRankSum=0.869;SOR=0.576;VQSLOD=-2.548e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:235,242:477:99:9340,0,8506
-chr6	57398207	rs71214816	G	T	3201.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.739;ClippingRankSum=0.609;DB;DP=476;FS=3.961;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-5.623;NEGATIVE_TRAIN_SITE;QD=6.73;ReadPosRankSum=0.211;SOR=0.475;VQSLOD=-3.396e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:358,113:471:99:3230,0,14267
-chr6	57398226	rs77436138	T	G	5638.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=6.880;ClippingRankSum=1.585;DB;DP=474;FS=4.176;MLEAC=1;MLEAF=0.500;MQ=55.11;MQ0=0;MQRankSum=-0.678;NEGATIVE_TRAIN_SITE;QD=11.90;ReadPosRankSum=-1.594;SOR=0.924;VQSLOD=-2.787e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:202,185:387:99:5667,0,7682
-chr6	57398264	rs62398998	A	G	10505.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=7.800;ClippingRankSum=0.363;DB;DP=483;FS=5.181;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-3.599;NEGATIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.128;SOR=0.919;VQSLOD=-2.719e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:185,297:482:99:10534,0,5426
-chr6	57398270	rs62398999	C	T	3777.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.082;ClippingRankSum=1.817;DB;DP=482;FS=4.566;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=0;MQRankSum=-2.615;NEGATIVE_TRAIN_SITE;QD=7.84;ReadPosRankSum=0.627;SOR=1.059;VQSLOD=-3.182e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:338,143:481:99:3806,0,12584
-chr6	57398335	rs4715745	A	T	7297.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=0.878;ClippingRankSum=-0.623;DB;DP=391;FS=18.280;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-1.096;NEGATIVE_TRAIN_SITE;QD=18.66;ReadPosRankSum=0.479;SOR=1.573;VQSLOD=-1.998e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:151,240:391:99:7326,0,4341
-chr6	57398385	rs11455120	A	AT	2033.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.004;ClippingRankSum=-0.159;DB;DP=270;FS=2.505;MLEAC=1;MLEAF=0.500;MQ=57.95;MQ0=0;MQRankSum=1.708;POSITIVE_TRAIN_SITE;QD=7.53;ReadPosRankSum=2.608;SOR=1.265;VQSLOD=-3.154e-01;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:165,71:236:99:2071,0,7214
-chr6	57398395	rs78658694	A	T	1426.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=5.633;ClippingRankSum=-0.557;DB;DP=246;FS=2.513;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=-1.385;NEGATIVE_TRAIN_SITE;QD=5.80;ReadPosRankSum=2.107;SOR=1.287;VQSLOD=-2.484e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:170,67:237:99:1455,0,7359
-chr6	57398412	rs6937166	A	G	1614.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=5.113;ClippingRankSum=0.840;DB;DP=201;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=0.045;NEGATIVE_TRAIN_SITE;QD=8.03;ReadPosRankSum=-0.110;SOR=0.142;VQSLOD=-1.257e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:145,56:201:99:1643,0,5481
-chr6	57398491	rs6937368	C	T	90.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.276;ClippingRankSum=0.170;DB;DP=40;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.019;QD=2.27;ReadPosRankSum=-0.511;SOR=0.039;VQSLOD=1.26;culprit=QD	GT:AD:DP:GQ:PL	0/1:34,6:40:99:119,0,1359
-chr6	57398503	rs4388290	A	G	387.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.279;ClippingRankSum=-0.151;DB;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.319;QD=10.77;ReadPosRankSum=-0.319;SOR=0.239;VQSLOD=2.63;culprit=FS	GT:AD:DP:GQ:PL	0/1:24,12:36:99:416,0,1055
-chr6	57398517	rs4400219	C	A	314.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.503;ClippingRankSum=0.370;DB;DP=31;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.196;QD=10.15;ReadPosRankSum=0.849;SOR=0.173;VQSLOD=3.45;culprit=FS	GT:AD:DP:GQ:PL	0/1:22,9:31:99:343,0,999
-chr6	57398587	rs4506046	A	G	226.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.635;ClippingRankSum=-0.831;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.977;QD=18.90;ReadPosRankSum=1.977;SOR=1.022;VQSLOD=3.22;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,7:12:99:255,0,157
-chr6	57398921	.	T	C	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:36:40,0,36
-chr6	57398943	rs12203062	C	T	29.77	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=7.44;ReadPosRankSum=-1.026;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:58:58,0,78
-chr6	57404528	rs12528027	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57404529	rs71221626	G	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57404548	rs6934525	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57404559	rs6911998	G	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409216	rs487488	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409238	rs7757807	T	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409250	rs28431347	T	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57409360	rs7775846	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57414331	rs522176	A	G	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57414352	rs522107	G	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57414355	rs577952	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57419091	rs11362490	AG	A	32.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=16.35;SOR=2.303;VQSLOD=8.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	57419145	rs482977	T	C	101.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.26;SOR=0.693;VQSLOD=7.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:129,12,0
-chr6	57419169	rs482916	C	T	96.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.09;SOR=1.179;VQSLOD=6.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	57419203	rs28444227	T	A	84.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.09;SOR=1.179;VQSLOD=6.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	57419529	rs5011343	C	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57419548	rs5011342	G	A	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.24;SOR=1.609;VQSLOD=4.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:70,6,0
-chr6	57419564	rs5011341	G	A	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57419593	rs5000703	G	T	60.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=6.82;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	57419621	rs5000702	C	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	57420055	rs973971	A	T	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	57420085	rs10678736	T	TGCAATA	43.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57420331	rs536921	A	G	45.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=11.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:33:74,0,33
-chr6	57420394	rs3903673	C	G	39.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.358;QD=7.95;ReadPosRankSum=1.231;SOR=1.609;VQSLOD=2.43;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,2:5:68:68,0,116
-chr6	57429628	rs9476125	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.39;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57429632	rs13200513	C	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57429655	rs13200414	A	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57429863	rs12194179	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57430291	rs12209094	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57430302	rs12195853	G	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57430787	rs9382792	A	G	66.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=5.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	57430868	rs9396334	C	T	14.68	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.68;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	57431267	rs2397534	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57436741	rs6924004	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57437720	rs519735	A	G	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=6.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	57437853	rs13212334	A	G	12.06	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:25:40,0,25
-chr6	57438133	rs1174361	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57438139	rs1174362	C	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57438156	rs78245671	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57440169	rs581096	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57440174	rs581102	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57440196	rs581193	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57440211	rs581228	T	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.37;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442438	rs5005193	C	G	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	57442463	rs5005192	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442488	rs4715782	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442506	rs5005191	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57442507	rs5005190	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57443228	rs6913239	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57443255	rs1855414	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57447972	rs4715787	T	G	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=6.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	57454558	rs9357983	C	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57454567	rs62399084	A	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57454589	rs9357984	A	G	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.54;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57454920	rs9357986	C	T	55.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=18.43;SOR=1.179;VQSLOD=5.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:83,9,0
-chr6	57455443	rs7766809	A	G	98.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.76;SOR=1.179;VQSLOD=6.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:126,9,0
-chr6	57456136	rs4596481	T	C	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.86;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	57456931	rs79510351	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57456963	rs75987787	T	C	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.05;SOR=1.179;VQSLOD=6.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57456968	rs78473260	G	A	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.40;SOR=1.179;VQSLOD=6.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:135,9,0
-chr6	57457564	rs3805802	A	G	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57461356	rs62399146	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57463643	rs6905367	A	G	45.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.87;SOR=2.303;VQSLOD=7.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:73,6,0
-chr6	57466787	rs6924157	G	C	81.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;QD=16.35;ReadPosRankSum=0.358;SOR=0.223;VQSLOD=5.23;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,3:5:59:110,0,59
-chr6	57466812	rs78692044	T	A	28.77	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=-0.720;QD=4.80;ReadPosRankSum=-0.720;SOR=1.179	GT:AD:DP:GQ:PL	0/1:4,2:6:57:57,0,146
-chr6	57466836	rs11411187	A	AC	203.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.067;ClippingRankSum=1.589;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=25.47;ReadPosRankSum=-1.067;SOR=0.693;VQSLOD=5.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,6:8:57:241,0,57
-chr6	57466844	rs12197381	G	A	64.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.573;ClippingRankSum=-0.573;DB;DP=9;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.248;QD=7.20;ReadPosRankSum=0.248;SOR=0.045;VQSLOD=0.706;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,3:9:93:93,0,212
-chr6	57466871	rs79082382	G	A	111.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.793;ClippingRankSum=0.244;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-2.141;QD=9.31;ReadPosRankSum=-0.529;SOR=0.446;VQSLOD=2.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,5:12:99:140,0,269
-chr6	57466891	rs12210717	A	T	431.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;ClippingRankSum=-0.698;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=-0.611;QD=20.56;ReadPosRankSum=0.349;SOR=0.941;VQSLOD=3.93;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,15:20:99:460,0,165
-chr6	57466915	rs12205876	T	A	732.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;ClippingRankSum=1.449;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=0.839;QD=26.17;ReadPosRankSum=1.297;SOR=0.402;VQSLOD=2.60;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:8,20:28:99:761,0,252
-chr6	57466922	rs2894917	T	C	1572.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.29;SOR=4.921;VQSLOD=6.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1601,111,0
-chr6	57466957	rs9885746	C	T	515.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;ClippingRankSum=-0.774;DB;DP=69;FS=3.021;MLEAC=1;MLEAF=0.500;MQ=57.62;MQ0=0;MQRankSum=-0.787;QD=7.47;ReadPosRankSum=-0.192;SOR=0.154;VQSLOD=-3.023e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:49,20:69:99:544,0,2169
-chr6	57466958	rs12212128	A	G	1712.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.269;ClippingRankSum=0.064;DB;DP=74;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=0;MQRankSum=-1.391;QD=23.15;ReadPosRankSum=-0.906;SOR=0.355;VQSLOD=2.47;culprit=FS	GT:AD:DP:GQ:PL	0/1:24,50:74:99:1741,0,776
-chr6	57466969	rs12212129	A	G	1088.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.620;ClippingRankSum=-0.340;DB;DP=83;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-0.237;QD=13.12;ReadPosRankSum=-0.386;SOR=0.362;VQSLOD=3.55;culprit=FS	GT:AD:DP:GQ:PL	0/1:50,33:83:99:1117,0,1689
-chr6	57466987	rs12205887	T	C	1230.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.854;ClippingRankSum=-0.004;DB;DP=98;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=0.575;QD=12.56;ReadPosRankSum=-0.126;SOR=0.389;VQSLOD=3.29;culprit=FS	GT:AD:DP:GQ:PL	0/1:58,40:98:99:1259,0,2007
-chr6	57467084	rs9885913	A	G	2211.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=4.628;ClippingRankSum=0.293;DB;DP=304;FS=4.869;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-0.944;NEGATIVE_TRAIN_SITE;QD=7.28;ReadPosRankSum=3.057;SOR=1.014;VQSLOD=-2.572e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:233,71:304:99:2240,0,9850
-chr6	57467093	rs9885916	A	G	2301.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=7.069;ClippingRankSum=0.184;DB;DP=312;FS=3.079;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-1.638;NEGATIVE_TRAIN_SITE;QD=7.38;ReadPosRankSum=0.912;SOR=0.918;VQSLOD=-2.342e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:239,73:312:99:2330,0,10451
-chr6	57467100	rs4535533	G	C	6947.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.106;ClippingRankSum=-2.135;DB;DP=314;FS=1.422;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-0.670;NEGATIVE_TRAIN_SITE;QD=22.13;ReadPosRankSum=0.520;SOR=0.800;VQSLOD=-1.704e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:122,192:314:99:6976,0,3683
-chr6	57467107	rs9885751	C	T	1881.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=6.859;ClippingRankSum=-1.729;DB;DP=314;FS=5.484;MLEAC=1;MLEAF=0.500;MQ=58.52;MQ0=0;MQRankSum=-1.808;NEGATIVE_TRAIN_SITE;QD=5.99;ReadPosRankSum=0.287;SOR=1.037;VQSLOD=-2.380e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:238,76:314:99:1910,0,9279
-chr6	57467175	rs4406234	A	G	2889.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.932;ClippingRankSum=-0.383;DB;DP=258;FS=0.469;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=0.153;NEGATIVE_TRAIN_SITE;QD=11.20;ReadPosRankSum=4.087;SOR=0.741;VQSLOD=-7.350e-01;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:159,99:258:99:2918,0,5132
-chr6	57467279	rs6459263	T	C	1140.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=5.633;ClippingRankSum=1.776;DB;DP=140;FS=4.536;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.542;NEGATIVE_TRAIN_SITE;QD=8.15;ReadPosRankSum=-0.103;SOR=0.269;VQSLOD=-1.496e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:104,36:140:99:1169,0,4245
-chr6	57467282	rs6459264	T	C	1140.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.755;ClippingRankSum=1.153;DB;DP=134;FS=1.319;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=1.020;POSITIVE_TRAIN_SITE;QD=8.51;ReadPosRankSum=-0.325;SOR=0.374;VQSLOD=1.58;culprit=QD	GT:AD:DP:GQ:PL	0/1:100,34:134:99:1169,0,4245
-chr6	57467303	rs1022846	A	G	3478.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=90;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.14;SOR=5.330;VQSLOD=6.74;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3507,271,0
-chr6	57467317	rs4637646	G	T	1210.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.996;ClippingRankSum=-0.892;DB;DP=73;FS=4.921;MLEAC=1;MLEAF=0.500;MQ=56.76;MQ0=0;MQRankSum=0.260;QD=16.59;ReadPosRankSum=0.593;SOR=0.140;VQSLOD=0.741;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,33:73:99:1239,0,1596
-chr6	57467323	rs4424069	G	C	1161.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.993;ClippingRankSum=-0.170;DB;DP=67;FS=4.828;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-0.107;QD=17.34;ReadPosRankSum=0.648;SOR=0.150;VQSLOD=0.857;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,31:67:99:1190,0,1431
-chr6	57467456	rs4358625	T	G	43.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=1.27;culprit=DP	GT:AD:DP:GQ:PL	0/1:1,2:3:31:72,0,31
-chr6	57472201	rs9885694	A	G	75.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.054;ClippingRankSum=-0.248;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.573;QD=8.42;ReadPosRankSum=1.683;SOR=0.283;VQSLOD=3.58;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,3:9:99:104,0,207
-chr6	57472212	rs9296899	T	A	251.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.531;ClippingRankSum=1.531;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.377;QD=22.89;ReadPosRankSum=0.382;SOR=1.802;VQSLOD=4.30;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,8:11:88:280,0,88
-chr6	57472255	rs9296900	C	T	533.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.047;ClippingRankSum=-1.484;DB;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.07;MQ0=0;MQRankSum=0.524;POSITIVE_TRAIN_SITE;QD=26.69;ReadPosRankSum=-0.786;SOR=2.093;VQSLOD=5.22;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,15:20:99:562,0,141
-chr6	57472299	rs9396358	A	G	360.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.622;ClippingRankSum=0.811;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-0.811;QD=10.61;ReadPosRankSum=-1.460;SOR=0.874;VQSLOD=2.75;culprit=FS	GT:AD:DP:GQ:PL	0/1:22,12:34:99:389,0,704
-chr6	57472315	rs9296901	A	G	1165.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.692;ClippingRankSum=-0.988;DB;DP=43;FS=2.613;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=0.663;QD=27.11;ReadPosRankSum=-1.151;SOR=0.271;VQSLOD=-5.021e-01;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:12,31:43:99:1194,0,341
-chr6	57472316	rs9382818	G	A	458.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.993;ClippingRankSum=-0.012;DB;DP=43;FS=2.578;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.360;QD=10.67;ReadPosRankSum=-1.950;SOR=0.156;VQSLOD=0.405;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:26,17:43:99:487,0,974
-chr6	57472344	rs111230027	A	AT	305.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.049;ClippingRankSum=0.230;DB;DP=64;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=1.887;POSITIVE_TRAIN_SITE;QD=4.78;ReadPosRankSum=-0.919;SOR=0.495;VQSLOD=5.04;culprit=FS	GT:AD:DP:GQ:PL	0/1:43,17:60:99:343,0,1062
-chr6	57472476	rs9382819	T	C	344.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.397;ClippingRankSum=1.197;DB;DP=44;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.718;QD=7.84;ReadPosRankSum=-1.021;SOR=1.226;VQSLOD=1.17;culprit=QD	GT:AD:DP:GQ:PL	0/1:30,14:44:99:373,0,1080
-chr6	57472488	rs9382820	C	T	419.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.192;ClippingRankSum=0.268;DB;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.395;QD=9.76;ReadPosRankSum=-1.949;SOR=0.836;VQSLOD=2.80;culprit=FS	GT:AD:DP:GQ:PL	0/1:28,15:43:99:448,0,1080
-chr6	57472495	rs62400219	C	G	263.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.265;ClippingRankSum=-0.448;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-0.215;QD=6.94;ReadPosRankSum=-0.050;SOR=0.481;VQSLOD=2.66;culprit=QD	GT:AD:DP:GQ:PL	0/1:28,10:38:99:292,0,1144
-chr6	57472533	rs9367767	T	C	332.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.122;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=-0.830;QD=19.57;ReadPosRankSum=0.049;SOR=0.330;VQSLOD=4.65;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,10:17:99:361,0,224
-chr6	57472534	rs74369127	T	C	46.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;ClippingRankSum=0.441;DB;DP=17;FS=7.533;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=0.189;NEGATIVE_TRAIN_SITE;QD=2.75;ReadPosRankSum=-1.449;SOR=0.010;VQSLOD=-1.589e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:14,3:17:75:75,0,661
-chr6	57474882	rs62400254	A	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.96;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57474896	rs62400255	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57476586	rs58187447	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57476608	rs57642151	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57479216	rs4530864	T	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.01;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57482492	rs12197718	T	C	39.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=19.87;SOR=2.303;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-chr6	57483749	rs9476179	C	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	57485342	rs9885648	T	C	10.20	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.804;QD=5.10;ReadPosRankSum=0.804;SOR=0.693	GT:AD:DP:GQ:PL	0/1:1,1:2:35:38,0,35
-chr6	57485391	rs1853495	T	G	15.65	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:42,3,0
-chr6	57490861	rs11963269	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57490866	rs9885704	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57491118	rs9885817	T	C	47.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.98;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:76,0,32
-chr6	57492741	rs79386390	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57492762	rs3805807	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57492776	rs77611141	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57493700	rs62404095	T	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.23;SOR=1.609;VQSLOD=6.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:86,6,0
-chr6	57493709	rs62404096	A	G	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=6.82;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	57493836	rs62404099	C	A	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57495024	rs5003525	A	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57495215	rs6939623	T	G	13.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.72;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:40,3,0
-chr6	57495238	rs62404102	T	C	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=5.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	57497543	rs6929435	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57497562	rs76224813	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57497579	rs73755610	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57498301	rs11754853	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57498324	rs11759488	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57498894	rs3846934	G	A	268.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.827;ClippingRankSum=0.059;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.884;QD=17.92;ReadPosRankSum=-0.177;SOR=1.112;VQSLOD=4.80;culprit=FS	GT:AD:DP:GQ:PL	0/1:6,9:15:99:297,0,200
-chr6	57498944	rs3846935	G	C	516.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;ClippingRankSum=-0.826;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.064;QD=17.23;ReadPosRankSum=0.233;SOR=0.784;VQSLOD=4.16;culprit=FS	GT:AD:DP:GQ:PL	0/1:12,18:30:99:545,0,370
-chr6	57499042	rs5876654	A	AT	87.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;ClippingRankSum=-0.570;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=3.51;ReadPosRankSum=-2.324;SOR=0.770;VQSLOD=4.42;culprit=FS	GT:AD:DP:GQ:PL	0/1:13,6:19:99:125,0,294
-chr6	57499171	rs3846936	T	C	122.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.731;QD=24.56;ReadPosRankSum=-0.731;SOR=1.981;VQSLOD=4.21;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,4:5:25:151,0,25
-chr6	57499188	rs2151627	C	T	39.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=13.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.90;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:28:68,0,28
-chr6	57499196	rs11423601	C	CA	24.75	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=63.51;MQ0=0;MQRankSum=0.736;QD=8.25;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:27:62,0,27
-chr6	57499926	rs2397610	A	G	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:35:40,0,35
-chr6	57500073	rs62404596	G	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=2.303;VQSLOD=6.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57500104	rs62404597	G	A	64.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=21.43;SOR=1.179;VQSLOD=6.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	57500169	rs6926645	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.37;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57500181	rs76287706	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=4.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57500197	rs11329134	GA	G	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57500204	rs78362714	C	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57500220	rs4537145	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57500442	rs4540266	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57503123	rs2397930	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57503159	rs3857631	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57503199	rs3996830	T	G	35.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.000;QD=8.94;ReadPosRankSum=-1.026;SOR=2.303;VQSLOD=4.04;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:64:64,0,64
-chr6	57503231	rs78058710	A	G	140.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=29.11;SOR=1.609;VQSLOD=4.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:168,12,0
-chr6	57503398	rs4995671	C	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.00;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57503441	rs4995670	T	A	94.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;QD=23.69;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.42;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:33:123,0,33
-chr6	57503444	rs11343070	AC	A	85.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.25;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:33:123,0,33
-chr6	57507333	rs148428624	C	T	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.87;SOR=2.303;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	57507431	rs139113051	T	C	11.83	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.83;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:38,3,0
-chr6	57507846	rs80010809	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57509520	rs62402976	C	T	41.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.87;SOR=0.693;VQSLOD=6.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-chr6	57511438	rs5011992	G	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=18.25;SOR=0.693;VQSLOD=6.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57511528	rs10592385	AATAAC	A	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=6.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57511564	rs5011994	G	A	50.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;QD=25.37;SOR=0.693;VQSLOD=6.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	57511607	rs77590924	C	T	14.68	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;QD=14.68;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	57511894	rs56224263	T	TAC	34.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.35;SOR=2.303;VQSLOD=8.87;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
-chr6	57512108	rs6914896	G	A	40.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=4.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:69:69,0,71
-chr6	57512340	rs4364484	C	T	502.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.633;ClippingRankSum=-0.142;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.217;QD=20.11;ReadPosRankSum=-0.311;SOR=1.358;VQSLOD=3.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,16:25:99:531,0,284
-chr6	57512352	rs5001077	A	T	198.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.659;ClippingRankSum=0.512;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.415;QD=6.63;ReadPosRankSum=-0.122;SOR=0.155;VQSLOD=2.84;culprit=QD	GT:AD:DP:GQ:PL	0/1:21,8:29:99:227,0,724
-chr6	57512439	rs4294006	T	C	1438.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=3.959;ClippingRankSum=0.864;DB;DP=144;FS=7.438;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-1.071;QD=9.99;ReadPosRankSum=0.578;SOR=0.083;VQSLOD=-7.791e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:95,49:144:99:1467,0,3234
-chr6	57512476	rs4307164	G	A	5505.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.662;ClippingRankSum=2.077;DB;DP=241;FS=1.012;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=1.460;NEGATIVE_TRAIN_SITE;QD=22.85;ReadPosRankSum=-2.015;SOR=0.914;VQSLOD=-1.923e+00;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:78,163:241:99:5534,0,2266
-chr6	57512510	rs4294007	T	G	13853.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=334;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.11;SOR=4.194;VQSLOD=3.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,334:334:99:13882,1010,0
-chr6	57512529	rs5001076	C	A	3081.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.175;ClippingRankSum=-2.050;DB;DP=368;FS=3.017;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.390;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=0.294;SOR=0.968;VQSLOD=-2.195e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:255,113:368:99:3110,0,8577
-chr6	57512565	rs4294008	T	C	9494.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=5.814;ClippingRankSum=0.828;DB;DP=416;FS=5.007;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=2.938;NEGATIVE_TRAIN_SITE;QD=22.82;ReadPosRankSum=-0.668;SOR=1.299;VQSLOD=-2.221e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:138,278:416:99:9523,0,3960
-chr6	57512678	rs4398719	G	A	11124.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=2.677;ClippingRankSum=0.517;DB;DP=458;FS=4.405;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=3.775;NEGATIVE_TRAIN_SITE;QD=24.29;ReadPosRankSum=-0.757;SOR=1.082;VQSLOD=-2.409e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:129,325:454:99:11153,0,3458
-chr6	57512711	rs5001484	G	C	5059.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=6.115;ClippingRankSum=-0.961;DB;DP=421;FS=6.509;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=0;MQRankSum=1.438;NEGATIVE_TRAIN_SITE;QD=12.02;ReadPosRankSum=0.324;SOR=1.225;VQSLOD=-1.980e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:267,138:405:99:5035,0,6158
-chr6	57512718	rs5001483	T	A	4671.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;ClippingRankSum=0.336;DB;DP=406;FS=3.080;MLEAC=1;MLEAF=0.500;MQ=52.12;MQ0=0;MQRankSum=0.364;NEGATIVE_TRAIN_SITE;QD=11.51;ReadPosRankSum=0.365;SOR=1.044;VQSLOD=-1.109e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:274,131:405:99:4700,0,11219
-chr6	57512740	.	CTGTTTT	C	1777.73	VQSRTrancheINDEL99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=0.374;ClippingRankSum=0.035;DP=356;FS=2.783;MLEAC=1;MLEAF=0.500;MQ=49.57;MQ0=0;MQRankSum=-7.250;NEGATIVE_TRAIN_SITE;QD=4.99;ReadPosRankSum=-0.198;SOR=0.328;VQSLOD=-3.212e+00;culprit=DP	GT:AD:DP:GQ:PL	0/1:286,64:350:99:1815,0,11798
-chr6	57512775	rs7773110	T	G	5490.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.254;ClippingRankSum=-0.905;DB;DP=233;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.06;MQ0=0;MQRankSum=-4.463;NEGATIVE_TRAIN_SITE;QD=23.57;ReadPosRankSum=-3.464;SOR=1.179;VQSLOD=-2.396e+00;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:92,138:230:99:5519,0,3342
-chr6	57512779	rs76296076	G	T	5369.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.880;ClippingRankSum=-0.404;DB;DP=218;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.59;MQ0=0;MQRankSum=-5.088;NEGATIVE_TRAIN_SITE;QD=24.63;ReadPosRankSum=-3.913;SOR=1.132;VQSLOD=-2.613e+00;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:89,129:218:99:5398,0,3366
-chr6	57512787	.	T	TCACCAAGGC	4709.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=4.158;ClippingRankSum=1.208;DP=186;FS=3.774;MLEAC=1;MLEAF=0.500;MQ=39.95;MQ0=0;MQRankSum=-6.907;QD=25.32;ReadPosRankSum=-2.737;SOR=2.176;VQSLOD=-1.452e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:78,108:186:99:4747,0,3127
-chr6	57512788	.	T	TTA	4547.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.353;ClippingRankSum=-0.603;DP=171;FS=3.354;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=0;MQRankSum=-7.416;QD=26.59;ReadPosRankSum=-1.258;SOR=1.878;VQSLOD=-9.837e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:79,92:171:99:4585,0,3055
-chr6	57512792	rs372064495	T	C	3372.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=7.455;ClippingRankSum=-0.198;DB;DP=157;FS=3.151;MLEAC=1;MLEAF=0.500;MQ=40.80;MQ0=0;MQRankSum=-6.089;NEGATIVE_TRAIN_SITE;QD=21.48;ReadPosRankSum=-0.528;SOR=1.733;VQSLOD=-1.961e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:76,81:157:99:3401,0,3097
-chr6	57512793	rs368894562	AATT	A	3279.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=7.041;ClippingRankSum=-0.005;DB;DP=158;FS=3.066;MLEAC=1;MLEAF=0.500;MQ=41.17;MQ0=0;MQRankSum=-7.628;QD=20.76;ReadPosRankSum=-0.270;SOR=1.670;VQSLOD=-9.290e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:78,80:158:99:3317,0,3097
-chr6	57512825	rs72880943	C	T	1989.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.227;ClippingRankSum=-1.068;DB;DP=102;FS=3.096;MLEAC=1;MLEAF=0.500;MQ=44.73;MQ0=0;MQRankSum=-6.811;NEGATIVE_TRAIN_SITE;QD=19.51;ReadPosRankSum=0.098;SOR=1.704;VQSLOD=-2.269e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:50,52:102:99:2018,0,1929
-chr6	57512826	rs7752845	A	G	1989.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=6.619;ClippingRankSum=1.207;DB;DP=100;FS=3.098;MLEAC=1;MLEAF=0.500;MQ=45.30;MQ0=0;MQRankSum=-6.799;NEGATIVE_TRAIN_SITE;QD=19.90;ReadPosRankSum=0.336;SOR=1.706;VQSLOD=-2.241e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:49,51:100:99:2018,0,1929
-chr6	57512841	rs78256005	A	G	630.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.056;ClippingRankSum=-0.094;DB;DP=79;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.16;MQ0=0;MQRankSum=-4.822;NEGATIVE_TRAIN_SITE;QD=7.98;ReadPosRankSum=-1.275;SOR=0.455;VQSLOD=-3.272e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:58,21:79:99:659,0,2392
-chr6	57512850	rs77911716	C	G	547.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=0.371;ClippingRankSum=-0.636;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.71;MQ0=0;MQRankSum=-4.402;NEGATIVE_TRAIN_SITE;QD=7.61;ReadPosRankSum=-1.021;SOR=0.357;VQSLOD=-2.865e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:55,17:72:99:576,0,2261
-chr6	57512874	rs71214002	G	A	206.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.499;ClippingRankSum=-0.194;DB;DP=49;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.30;MQ0=0;MQRankSum=-1.846;QD=4.22;ReadPosRankSum=1.072;SOR=0.058;VQSLOD=0.727;culprit=QD	GT:AD:DP:GQ:PL	0/1:40,9:49:99:235,0,1573
-chr6	57512889	rs75351177	C	T	149.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.464;ClippingRankSum=-0.226;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=-2.862;QD=3.94;ReadPosRankSum=-1.167;SOR=0.061;VQSLOD=-8.131e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:31,7:38:99:178,0,1252
-chr6	57512893	rs77348569	C	T	175.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.044;ClippingRankSum=0.000;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.45;MQ0=0;MQRankSum=-2.215;QD=5.17;ReadPosRankSum=-0.852;SOR=0.078;VQSLOD=0.483;culprit=QD	GT:AD:DP:GQ:PL	0/1:27,7:34:99:204,0,1222
-chr6	57512902	rs77563921	G	A	112.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.759;ClippingRankSum=0.900;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-1.860;QD=4.03;ReadPosRankSum=-1.140;SOR=0.061;VQSLOD=0.509;culprit=QD	GT:AD:DP:GQ:PL	0/1:23,5:28:99:141,0,951
-chr6	57512903	rs75209982	C	A	112.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.939;ClippingRankSum=-1.560;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-2.939;QD=4.03;ReadPosRankSum=-1.500;SOR=0.061;VQSLOD=-8.813e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:23,5:28:99:141,0,951
-chr6	57512906	rs77519815	T	A	337.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.628;ClippingRankSum=1.732;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.72;MQ0=0;MQRankSum=-3.289;QD=12.51;ReadPosRankSum=-2.536;SOR=0.317;VQSLOD=-8.036e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:17,10:27:99:366,0,726
-chr6	57512916	rs140176282	A	AT	70.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;ClippingRankSum=-0.191;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.71;MQ0=0;MQRankSum=-1.244;QD=3.22;ReadPosRankSum=-0.670;SOR=0.039;VQSLOD=4.77;culprit=FS	GT:AD:DP:GQ:PL	0/1:19,3:22:99:108,0,828
-chr6	57513042	rs76730673	C	T	87.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=29.09;SOR=1.179;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:115,9,0
-chr6	57514007	rs4712214	A	G	66.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=7.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	57514048	rs79485395	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57517722	rs75802839	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.87;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.43;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57517733	rs80270590	T	A	96.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.10;MQ0=0;QD=32.09;SOR=2.833;VQSLOD=6.48;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:124,9,0
-chr6	57517777	rs76191741	A	G	19.81	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=0;MQRankSum=1.026;QD=3.96;ReadPosRankSum=0.000;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:37:48,0,37
-chr6	57517837	rs79522959	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57517838	rs1853506	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.00;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57517853	rs76412158	A	T	10.90	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.90;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:37,3,0
-chr6	57518157	rs4993255	T	C	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	57519294	rs5017411	C	G	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57519302	rs79076980	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57519303	rs74656916	A	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57519820	rs7744217	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57521340	rs73755643	C	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57521352	rs74795344	A	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.08;SOR=1.609;VQSLOD=6.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:90,6,0
-chr6	57521365	rs76281818	G	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57521370	rs61198018	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.32;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522688	rs76632457	T	C	24.78	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=8.26;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:53,0,33
-chr6	57522722	rs80202467	G	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522729	rs76599881	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522740	rs78027687	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.91;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57522743	rs72880950	G	A	52.78	PASS	AC=1;AF=0.500;AN=2;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQ0=0;QD=26.39;SOR=0.693;VQSLOD=7.37;culprit=FS	GT:AD:DP:GQ:PL	0/1:0,2:2:26:81,0,26
-chr6	57522745	rs79247610	A	C	52.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.84;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:26:81,0,26
-chr6	57526215	rs5019459	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57526220	rs5019458	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57526231	rs5019457	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57526585	rs62405765	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57526610	rs4370353	C	T	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.16;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57527149	rs77487282	A	C	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	57528643	rs4989228	G	A	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	57529061	rs4580853	C	T	46.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=23.37;SOR=0.693;VQSLOD=7.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	57529121	rs4236160	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57531762	rs2894929	A	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=0;QD=6.20;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57531763	rs4537146	G	A	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=0;QD=6.20;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57536087	rs77762742	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57536105	rs77828016	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57538839	rs78941520	C	T	43.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=14.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:72,0,32
-chr6	57538866	rs80259399	C	T	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.77;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,118
-chr6	57538867	rs75525472	A	G	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=4.75;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:78:78,0,118
-chr6	57538878	rs62405823	G	A	86.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=21.69;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.39;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:29:115,0,29
-chr6	57539231	rs73753049	C	T	11.12	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447	GT:AD:DP:GQ:PL	0/1:1,1:2:34:39,0,34
-chr6	57539244	rs77110690	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539245	rs150830310	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539260	rs73753050	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539457	rs62405831	G	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539460	rs35133381	AT	A	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.63;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57539480	rs2498202	T	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=6.95;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57544039	rs2498209	C	G	60.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=7.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:88,9,0
-chr6	57546228	rs12212539	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546230	rs77288943	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.02;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546234	rs12205399	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.35;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546244	rs79029147	C	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57546251	rs78287808	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=32.99;SOR=1.609;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:90,6,0
-chr6	57546252	rs74936228	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=30.52;SOR=1.609;VQSLOD=6.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:90,6,0
-chr6	57546590	rs1853496	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57547418	rs76051348	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57547428	rs76625067	C	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57549247	rs2476489	C	G	16.63	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.63;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:43,3,0
-chr6	57550746	rs74923423	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57550797	rs78408847	G	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	57556582	rs2397904	C	T	14.68	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.68;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	57556703	rs2397905	G	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	57556977	rs113627621	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57556995	rs113330746	A	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57557004	rs4425585	C	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57560942	rs3903831	C	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57560949	rs4097974	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57562969	rs77727649	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57564830	rs78356131	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57564831	rs77336271	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57564861	rs6932761	T	C	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=6.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	57565509	rs11965356	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57570509	rs78347797	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57570530	rs6903247	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57574113	rs5008152	G	A	71.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	57574138	rs5008153	T	A	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.43;SOR=1.179;VQSLOD=6.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	57576825	rs73755103	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57576836	rs73755104	T	G	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57576845	rs73755105	C	G	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57595707	rs72871580	T	C	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.61;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57595709	rs72871582	C	T	52.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:81,0,36
-chr6	57595723	rs75919230	C	G	83.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.77;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:33:112,0,33
-chr6	57595732	rs72871584	G	T	83.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:33:112,0,33
-chr6	57595770	rs73756249	A	G	34.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.000;QD=8.69;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=4.24;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:37:63,0,37
-chr6	57595781	rs73457550	G	A	33.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.000;QD=8.44;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=3.90;culprit=QD	GT:AD:DP:GQ:PL	0/1:2,2:4:37:62,0,37
-chr6	57595820	rs73756251	T	G	76.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=19.19;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.66;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:29:105,0,29
-chr6	57595832	rs77557182	T	C	11.12	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447	GT:AD:DP:GQ:PL	0/1:1,1:2:39:39,0,39
-chr6	57595845	rs76008427	A	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57597257	rs72871594	A	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=7.04;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	57597260	rs72871595	A	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=30.27;SOR=1.609;VQSLOD=6.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,1:1:6:79,6,0
-chr6	57603832	rs80257130	A	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57603839	rs147344208	A	AT	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57603845	rs72873407	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.34;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57606933	rs73757604	T	C	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.85;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	57606965	rs74644238	T	G	66.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:94,9,0
-chr6	57606996	rs73459287	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57607035	rs73757606	G	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.07;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57607044	rs73757607	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.28;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	57607068	rs72873457	C	T	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57607074	rs4360139	G	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	57608079	rs73459299	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57612661	.	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57618295	rs5876690	G	GA	25.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.86;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:62,6,0
-chr6	57673397	rs7765475	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57686962	rs140945786	G	T	100.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.550;POSITIVE_TRAIN_SITE;QD=14.40;ReadPosRankSum=0.937;SOR=3.221;VQSLOD=0.651;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:99:129,0,102
-chr6	57699097	rs6459305	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57710858	rs149357140	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57711844	rs143767848	A	T	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=8.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	57723952	rs11295509	CA	C	37.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.42;SOR=1.179;VQSLOD=5.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:74,9,0
-chr6	57732063	.	C	A	12.13	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=3.03;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:17:40,0,17
-chr6	57737999	rs142093663	G	A	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=27.87;SOR=0.693;VQSLOD=6.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	57738613	.	C	T	20.78	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	57785184	rs116169256	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57826827	.	TA	T	24.72	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.24;MQ0=0;QD=12.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	57841273	rs188364530	C	T	1364.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.628;ClippingRankSum=0.296;DB;DP=85;FS=7.134;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=1.622;POSITIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-0.110;SOR=0.843;VQSLOD=1.24;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1393,0,1205
-chr6	57841320	rs140816261	G	T	1315.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.878;ClippingRankSum=-0.287;DB;DP=83;FS=5.670;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-0.132;POSITIVE_TRAIN_SITE;QD=15.85;ReadPosRankSum=-0.515;SOR=1.312;VQSLOD=1.62;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,43:83:99:1344,0,1358
-chr6	57841627	rs149540211	AC	A	954.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;ClippingRankSum=0.306;DB;DP=80;FS=3.046;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=1.819;QD=11.93;ReadPosRankSum=-1.129;SOR=0.798;VQSLOD=0.740;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:42,36:78:99:992,0,1172
-chr6	57842518	rs149985050	G	T	70.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.000;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=10.11;ReadPosRankSum=0.937;SOR=0.495;VQSLOD=5.83;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,3:7:99:99,0,144
-chr6	57843574	rs115026909	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57857856	rs3000344	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	57972306	rs55752203	TG	T	24.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=12.36;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-chr6	57977600	rs115553313	C	T	97.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=1.179;VQSLOD=8.27;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:125,9,0
-chr6	57977640	rs4960490	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	57998262	rs9476413	T	C	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=6.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	58028492	rs147632909	C	A	37.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=9.44;ReadPosRankSum=0.000;SOR=2.303;VQSLOD=5.34;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:66:66,0,74
-chr6	58039789	rs9382925	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58165037	.	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	58165039	.	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.45;culprit=DP	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	58165065	.	GT	G	53.70	PASS	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	58173632	rs114670858	T	G	20.78	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	58246055	rs6918567	T	C	2357.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.591;ClippingRankSum=-0.427;DB;DP=249;FS=6.315;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=0;MQRankSum=-11.921;POSITIVE_TRAIN_SITE;QD=9.47;ReadPosRankSum=2.161;SOR=1.112;VQSLOD=-3.174e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:179,69:248:99:2386,0,8176
-chr6	58246056	rs6930828	G	A	2357.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.659;ClippingRankSum=0.056;DB;DP=250;FS=5.251;MLEAC=1;MLEAF=0.500;MQ=50.59;MQ0=0;MQRankSum=-11.878;QD=9.43;ReadPosRankSum=-0.007;SOR=1.079;VQSLOD=-4.553e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:179,70:249:99:2386,0,8176
-chr6	58246143	rs6931014	G	A	3997.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;ClippingRankSum=-0.730;DB;DP=326;FS=0.849;MLEAC=1;MLEAF=0.500;MQ=49.42;MQ0=0;MQRankSum=-4.926;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=3.641;SOR=0.631;VQSLOD=-1.659e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:186,138:324:99:4026,0,5840
-chr6	58250570	rs9500243	A	T	402.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.537;ClippingRankSum=0.754;DB;DP=40;FS=8.709;MLEAC=1;MLEAF=0.500;MQ=50.10;MQ0=0;MQRankSum=0.698;POSITIVE_TRAIN_SITE;QD=10.07;ReadPosRankSum=0.112;SOR=0.032;VQSLOD=1.36;culprit=FS	GT:AD:DP:GQ:PL	0/1:25,15:40:99:431,0,789
-chr6	58252949	.	A	G	37.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.322;ClippingRankSum=-0.684;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.30;MQ0=0;MQRankSum=-0.684;QD=4.72;ReadPosRankSum=0.322;SOR=0.368;VQSLOD=3.52;culprit=QD	GT:AD:DP:GQ:PL	0/1:5,3:8:66:66,0,144
-chr6	58260059	rs74657950	G	A	177.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.067;ClippingRankSum=0.058;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.79;MQ0=0;MQRankSum=-2.025;QD=11.85;ReadPosRankSum=0.984;SOR=0.582;VQSLOD=2.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:8,7:15:99:206,0,240
-chr6	58260138	rs62464086	A	G	246.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;ClippingRankSum=-0.921;DB;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-2.308;QD=5.74;ReadPosRankSum=0.921;SOR=0.569;VQSLOD=0.439;culprit=QD	GT:AD:DP:GQ:PL	0/1:28,14:42:99:275,0,785
-chr6	58263609	rs4079740	A	G	17.84	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQ0=0;MQRankSum=-1.231;QD=3.57;ReadPosRankSum=0.358;SOR=0.446	GT:AD:DP:GQ:PL	0/1:3,2:5:46:46,0,99
-chr6	58263871	rs6588681	T	C	325.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.892;ClippingRankSum=-0.055;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=0;MQRankSum=-2.022;QD=9.87;ReadPosRankSum=1.730;SOR=0.941;VQSLOD=1.68;culprit=FS	GT:AD:DP:GQ:PL	0/1:19,14:33:99:354,0,577
-chr6	58263932	rs1810425	G	A	548.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.642;ClippingRankSum=-0.644;DB;DP=42;FS=1.298;MLEAC=1;MLEAF=0.500;MQ=56.18;MQ0=0;MQRankSum=-0.407;QD=13.07;ReadPosRankSum=-0.223;SOR=1.002;VQSLOD=1.43;culprit=FS	GT:AD:DP:GQ:PL	0/1:23,18:41:99:577,0,758
-chr6	58263952	rs1810426	A	G	478.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.162;ClippingRankSum=-0.058;DB;DP=46;FS=2.893;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=0;MQRankSum=1.471;QD=10.41;ReadPosRankSum=0.683;SOR=1.251;VQSLOD=1.23;culprit=QD	GT:AD:DP:GQ:PL	0/1:27,18:45:99:507,0,927
-chr6	58265128	rs9391382	T	C	346.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;ClippingRankSum=-0.596;DB;DP=54;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.99;MQ0=0;MQRankSum=-5.275;NEGATIVE_TRAIN_SITE;QD=6.42;ReadPosRankSum=-1.037;SOR=0.793;VQSLOD=-3.620e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:36,18:54:99:375,0,1179
-chr6	58265398	rs17488291	G	A	1245.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.662;ClippingRankSum=0.505;DB;DP=89;FS=7.385;MLEAC=1;MLEAF=0.500;MQ=53.47;MQ0=0;MQRankSum=-1.229;POSITIVE_TRAIN_SITE;QD=14.00;ReadPosRankSum=1.648;SOR=1.478;VQSLOD=1.83;culprit=FS	GT:AD:DP:GQ:PL	0/1:47,42:89:99:1274,0,1450
-chr6	58265469	.	G	GTTT	400.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;ClippingRankSum=1.203;DP=68;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.92;MQ0=0;MQRankSum=-3.451;QD=5.89;ReadPosRankSum=-0.359;SOR=0.651;VQSLOD=1.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,19:53:99:438,0,1230
-chr6	58273526	rs4928423	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58287821	rs9404620	A	G	128.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.307;ClippingRankSum=0.876;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.729;POSITIVE_TRAIN_SITE;QD=14.31;ReadPosRankSum=0.000;SOR=0.892;VQSLOD=6.42;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:157,0,118
-chr6	58294828	rs2012049	C	T	129.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.663;ClippingRankSum=-0.251;DB;DP=17;FS=2.884;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=0;MQRankSum=-2.161;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=-0.151;SOR=1.688;VQSLOD=0.937;culprit=QD	GT:AD:DP:GQ:PL	0/1:11,6:17:99:158,0,414
-chr6	58302194	rs693484	T	A	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.67;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	58365506	rs60186309	T	TA	41.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.85;SOR=0.693;VQSLOD=8.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:78,6,0
-chr6	58447068	rs1224740	A	G	1017.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.800;ClippingRankSum=-0.222;DB;DP=64;FS=3.511;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=15.90;ReadPosRankSum=-0.356;SOR=1.296;VQSLOD=3.10;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:32,32:64:99:1046,0,1021
-chr6	58465552	rs1224802	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.51;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58490384	rs7770844	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58693830	rs2343003	A	C	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	58735978	rs2343014	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	58776289	rs4357163	T	G	186.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.202;ClippingRankSum=0.775;DB;DP=26;FS=2.192;MLEAC=1;MLEAF=0.500;MQ=33.30;MQ0=0;MQRankSum=-1.085;QD=7.18;ReadPosRankSum=0.837;SOR=1.460;VQSLOD=0.168;culprit=QD	GT:AD:DP:GQ:PL	0/1:13,10:23:99:215,0,418
-chr6	58776318	rs9986349	A	G	261.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.368;ClippingRankSum=-0.152;DB;DP=22;FS=2.098;MLEAC=1;MLEAF=0.500;MQ=32.68;MQ0=0;MQRankSum=-0.684;QD=11.90;ReadPosRankSum=-0.304;SOR=0.243;VQSLOD=1.18;culprit=QD	GT:AD:DP:GQ:PL	0/1:11,9:20:99:290,0,435
-chr6	58776319	rs9638012	C	T	871.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.68;MQ0=0;QD=28.76;SOR=2.093;VQSLOD=5.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,20:20:60:900,60,0
-chr6	58776352	rs4317432	T	C	267.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.799;ClippingRankSum=-0.318;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.04;MQ0=0;MQRankSum=-0.847;QD=15.75;ReadPosRankSum=-1.059;SOR=0.653;VQSLOD=4.28;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,9:16:99:296,0,314
-chr6	58776411	rs9638013	A	G	364.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.887;ClippingRankSum=-1.415;DB;DP=18;FS=2.846;MLEAC=1;MLEAF=0.500;MQ=28.44;MQ0=0;MQRankSum=-0.283;QD=20.26;ReadPosRankSum=0.962;SOR=0.148;VQSLOD=1.19;culprit=QD	GT:AD:DP:GQ:PL	0/1:4,13:17:99:393,0,132
-chr6	58776442	rs9638019	T	C	491.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;ClippingRankSum=0.381;DB;DP=25;FS=2.593;MLEAC=1;MLEAF=0.500;MQ=35.87;MQ0=0;MQRankSum=-0.498;QD=19.67;ReadPosRankSum=0.088;SOR=1.863;VQSLOD=1.35;culprit=QD	GT:AD:DP:GQ:PL	0/1:10,14:24:99:520,0,292
-chr6	58776542	rs4524636	G	A	45.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.367;ClippingRankSum=0.115;DB;DP=64;FS=1.496;MLEAC=1;MLEAF=0.500;MQ=48.96;MQ0=0;MQRankSum=0.136;NEGATIVE_TRAIN_SITE;QD=0.72;ReadPosRankSum=-0.073;SOR=1.179;VQSLOD=-1.126e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:54,8:62:74:74,0,1805
-chr6	58776555	rs4928523	T	C	742.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.227;ClippingRankSum=-0.403;DB;DP=63;FS=9.224;MLEAC=1;MLEAF=0.500;MQ=49.77;MQ0=0;MQRankSum=0.433;QD=11.79;ReadPosRankSum=1.884;SOR=1.229;VQSLOD=4.000e-03;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,25:61:99:771,0,1202
-chr6	58776592	rs9377908	A	G	222.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.650;ClippingRankSum=-0.434;DB;DP=74;FS=1.153;MLEAC=1;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=0.889;NEGATIVE_TRAIN_SITE;QD=3.01;ReadPosRankSum=0.918;SOR=0.460;VQSLOD=-9.187e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:58,14:72:99:251,0,2116
-chr6	58776745	rs9632507	C	T	3168.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.29;MQ0=0;QD=32.18;SOR=0.927;VQSLOD=5.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3197,226,0
-chr6	58776782	rs9632508	A	T	3215.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.76;MQ0=0;QD=30.10;SOR=0.887;VQSLOD=5.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3244,240,0
-chr6	58776802	rs4401693	T	G	670.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;ClippingRankSum=-0.171;DB;DP=80;FS=3.349;MLEAC=1;MLEAF=0.500;MQ=54.82;MQ0=0;MQRankSum=2.069;QD=8.38;ReadPosRankSum=0.137;SOR=1.112;VQSLOD=-5.951e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:49,25:74:99:699,0,1658
-chr6	58776855	rs4928552	A	G	1233.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;ClippingRankSum=0.370;DB;DP=79;FS=1.923;MLEAC=1;MLEAF=0.500;MQ=54.95;MQ0=0;MQRankSum=1.187;QD=15.62;ReadPosRankSum=-0.469;SOR=0.872;VQSLOD=1.36;culprit=DP	GT:AD:DP:GQ:PL	0/1:35,38:73:99:1262,0,1231
-chr6	58776887	rs113904338	A	G	105.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=3.374;ClippingRankSum=-1.479;DB;DP=74;FS=1.493;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=1.286;NEGATIVE_TRAIN_SITE;QD=1.43;ReadPosRankSum=1.305;SOR=1.159;VQSLOD=-1.368e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:59,8:67:99:134,0,2069
-chr6	58776958	rs4562168	A	T	38.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.772;ClippingRankSum=1.153;DB;DP=68;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=0.582;QD=0.57;ReadPosRankSum=1.725;SOR=0.941;VQSLOD=0.880;culprit=QD	GT:AD:DP:GQ:PL	0/1:58,7:65:67:67,0,2198
-chr6	58776965	rs9632509	C	T	18.82	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.964;ClippingRankSum=-1.381;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=1.202;QD=0.26;ReadPosRankSum=1.441;SOR=0.796	GT:AD:DP:GQ:PL	0/1:62,7:69:47:47,0,2234
-chr6	58776982	rs9632510	G	T	1497.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.267;ClippingRankSum=0.065;DB;DP=67;FS=1.041;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=-0.411;QD=22.35;ReadPosRankSum=-0.887;SOR=0.510;VQSLOD=-2.878e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:19,46:65:99:1526,0,547
-chr6	58776984	rs56092323	A	T	39.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.000;ClippingRankSum=0.603;DB;DP=67;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=1.386;QD=0.59;ReadPosRankSum=1.323;SOR=0.787;VQSLOD=0.978;culprit=QD	GT:AD:DP:GQ:PL	0/1:58,7:65:68:68,0,2352
-chr6	58777039	rs28781680	G	A	376.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.782;ClippingRankSum=-0.924;DB;DP=63;FS=4.123;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=1.682;QD=5.98;ReadPosRankSum=-0.766;SOR=1.179;VQSLOD=-5.013e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:47,16:63:99:405,0,1853
-chr6	58777056	rs9654654	G	T	772.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.293;ClippingRankSum=0.839;DB;DP=64;FS=5.150;MLEAC=1;MLEAF=0.500;MQ=45.93;MQ0=0;MQRankSum=1.899;QD=12.07;ReadPosRankSum=-0.041;SOR=1.004;VQSLOD=0.153;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:39,25:64:99:801,0,1404
-chr6	58777074	rs4388312	C	T	822.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;ClippingRankSum=-1.281;DB;DP=65;FS=6.614;MLEAC=1;MLEAF=0.500;MQ=49.69;MQ0=0;MQRankSum=0.164;QD=12.66;ReadPosRankSum=-1.018;SOR=0.612;VQSLOD=0.293;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,31:65:99:851,0,1154
-chr6	58777106	rs4610595	A	G	643.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;ClippingRankSum=1.422;DB;DP=67;FS=5.024;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-0.611;QD=9.61;ReadPosRankSum=0.573;SOR=0.565;VQSLOD=0.035;culprit=QD	GT:AD:DP:GQ:PL	0/1:41,26:67:99:672,0,1465
-chr6	58777109	rs9647639	C	T	510.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.158;ClippingRankSum=0.783;DB;DP=69;FS=9.064;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.783;NEGATIVE_TRAIN_SITE;QD=7.40;ReadPosRankSum=-1.203;SOR=1.679;VQSLOD=-1.890e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:46,23:69:99:539,0,1603
-chr6	58777156	rs4577825	C	G	121.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;ClippingRankSum=0.330;DB;DP=81;FS=4.661;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=0;MQRankSum=1.120;NEGATIVE_TRAIN_SITE;QD=1.50;ReadPosRankSum=-0.258;SOR=1.196;VQSLOD=-2.068e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:67,11:78:99:150,0,2400
-chr6	58777178	rs9638022	G	T	2960.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.64;MQ0=0;QD=28.06;SOR=0.774;VQSLOD=5.10;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2989,229,0
-chr6	58777233	rs4336468	C	T	554.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.430;ClippingRankSum=-1.640;DB;DP=65;FS=1.047;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=0.052;QD=8.53;ReadPosRankSum=0.696;SOR=0.914;VQSLOD=0.514;culprit=QD	GT:AD:DP:GQ:PL	0/1:44,19:63:99:583,0,1593
-chr6	58777237	rs4518527	A	G	633.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.144;ClippingRankSum=0.639;DB;DP=59;FS=5.406;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.634;QD=10.74;ReadPosRankSum=-0.971;SOR=0.569;VQSLOD=-4.540e-02;culprit=QD	GT:AD:DP:GQ:PL	0/1:34,24:58:99:662,0,1277
-chr6	58777276	rs4446588	A	C	897.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.100;ClippingRankSum=0.236;DB;DP=62;FS=0.990;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=1.879;QD=14.48;ReadPosRankSum=0.023;SOR=0.662;VQSLOD=0.954;culprit=FS	GT:AD:DP:GQ:PL	0/1:32,27:59:99:926,0,946
-chr6	58777295	rs9638023	T	C	2798.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.73;MQ0=0;QD=33.48;SOR=0.790;VQSLOD=5.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2827,196,0
-chr6	58777312	rs9632511	T	C	759.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;ClippingRankSum=-1.050;DB;DP=72;FS=11.531;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=0;MQRankSum=-1.776;QD=10.55;ReadPosRankSum=0.984;SOR=1.631;VQSLOD=-1.664e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:44,23:67:99:788,0,1478
-chr6	58777366	rs9632513	A	G	2731.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;QD=29.84;SOR=0.756;VQSLOD=5.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2760,199,0
-chr6	58777546	rs9632515	G	A	2432.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.61;MQ0=0;QD=30.91;SOR=0.723;VQSLOD=5.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,67:67:99:2461,201,0
-chr6	58777573	rs9632516	C	T	2295.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.251;ClippingRankSum=1.138;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;MQRankSum=-0.559;NEGATIVE_TRAIN_SITE;QD=34.78;ReadPosRankSum=1.794;SOR=0.826;VQSLOD=-6.277e-01;culprit=QD	GT:AD:DP:GQ:PL	1/1:2,62:64:99:2324,117,0
-chr6	58777583	rs4351287	A	G	250.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.157;ClippingRankSum=0.238;DB;DP=69;FS=1.199;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-0.221;QD=3.63;ReadPosRankSum=0.648;SOR=0.717;VQSLOD=-7.794e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:52,13:65:99:279,0,1731
-chr6	58777599	.	T	G	144.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=0.474;ClippingRankSum=-0.957;DP=71;FS=5.022;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=-0.563;NEGATIVE_TRAIN_SITE;QD=2.04;ReadPosRankSum=-0.063;SOR=0.899;VQSLOD=-1.822e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:56,10:66:99:173,0,1929
-chr6	58777775	.	A	C	471.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;ClippingRankSum=0.625;DP=64;FS=1.059;MLEAC=1;MLEAF=0.500;MQ=56.10;MQ0=0;MQRankSum=0.170;QD=7.37;ReadPosRankSum=1.517;SOR=0.904;VQSLOD=0.168;culprit=QD	GT:AD:DP:GQ:PL	0/1:40,19:59:99:500,0,1465
-chr6	58777789	rs4296911	T	C	850.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;ClippingRankSum=-0.201;DB;DP=67;FS=8.737;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=0.892;QD=12.70;ReadPosRankSum=-2.082;SOR=0.733;VQSLOD=-2.447e-01;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:35,28:63:99:879,0,1323
-chr6	58777828	rs11211786	G	A	652.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.463;ClippingRankSum=-0.018;DB;DP=77;FS=10.707;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=2.081;NEGATIVE_TRAIN_SITE;QD=8.48;ReadPosRankSum=-0.651;SOR=1.322;VQSLOD=-1.674e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:46,26:72:99:681,0,1420
-chr6	58777836	rs9632517	A	C	2870.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.16;MQ0=0;QD=28.37;SOR=0.811;VQSLOD=2.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2899,214,0
-chr6	58777939	rs9632518	G	A	2463.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.89;MQ0=0;QD=25.14;SOR=1.143;VQSLOD=4.33;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2492,187,0
-chr6	58777952	rs4546514	A	G	853.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.230;ClippingRankSum=-1.282;DB;DP=63;FS=2.122;MLEAC=1;MLEAF=0.500;MQ=43.01;MQ0=0;MQRankSum=1.134;QD=13.55;ReadPosRankSum=2.245;SOR=0.460;VQSLOD=1.24;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:28,32:60:99:882,0,851
-chr6	58778001	.	G	A	533.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.458;ClippingRankSum=-0.800;DP=68;FS=0.981;MLEAC=1;MLEAF=0.500;MQ=45.56;MQ0=0;MQRankSum=-0.598;QD=7.85;ReadPosRankSum=0.699;SOR=0.563;VQSLOD=-6.300e-02;culprit=QD	GT:AD:DP:GQ:PL	0/1:41,22:63:99:562,0,1296
-chr6	58778019	rs9638027	T	G	165.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.004;ClippingRankSum=-1.301;DB;DP=72;FS=1.422;MLEAC=1;MLEAF=0.500;MQ=45.92;MQ0=0;MQRankSum=1.339;NEGATIVE_TRAIN_SITE;QD=2.30;ReadPosRankSum=0.522;SOR=1.106;VQSLOD=-1.041e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:56,9:65:99:194,0,2191
-chr6	58778025	rs9638028	A	G	2317.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.876;ClippingRankSum=-0.113;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=0;MQRankSum=-0.523;QD=32.19;ReadPosRankSum=0.277;SOR=0.604;VQSLOD=0.716;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,60:67:99:2346,0,110
-chr6	58778036	rs9404685	A	C	534.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.105;ClippingRankSum=-1.103;DB;DP=69;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.49;MQ0=0;MQRankSum=-0.499;QD=7.75;ReadPosRankSum=1.173;SOR=0.668;VQSLOD=2.83;culprit=QD	GT:AD:DP:GQ:PL	0/1:38,25:63:99:563,0,1164
-chr6	58778039	rs9638014	G	C	2754.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.01;MQ0=0;QD=30.33;SOR=0.790;VQSLOD=5.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2783,190,0
-chr6	58778081	rs4389792	T	G	2804.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.55;MQ0=0;QD=36.83;SOR=0.865;VQSLOD=3.57;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2833,190,0
-chr6	58778082	rs4346876	T	C	2759.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.55;MQ0=0;QD=35.85;SOR=0.865;VQSLOD=5.04;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2788,187,0
-chr6	58778100	rs9391506	A	T	94.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;ClippingRankSum=-0.536;DB;DP=63;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=0;MQRankSum=-0.098;QD=1.50;ReadPosRankSum=-0.930;SOR=0.801;VQSLOD=0.858;culprit=QD	GT:AD:DP:GQ:PL	0/1:48,9:57:99:123,0,1551
-chr6	58778108	rs4308591	G	C	2796.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.20;MQ0=0;QD=21.44;SOR=1.092;VQSLOD=3.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2825,196,0
-chr6	58778145	rs9500568	T	C	228.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;ClippingRankSum=0.435;DB;DP=69;FS=1.229;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=0.074;QD=3.32;ReadPosRankSum=0.631;SOR=0.425;VQSLOD=-7.171e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:52,13:65:99:257,0,1648
-chr6	58778148	rs12213271	T	C	43.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.529;ClippingRankSum=0.210;DB;DP=69;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=-2.466;NEGATIVE_TRAIN_SITE;QD=0.63;ReadPosRankSum=-1.168;SOR=0.796;VQSLOD=-1.747e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:57,8:65:72:72,0,1899
-chr6	58778190	rs9767581	T	G	325.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.002;ClippingRankSum=-0.571;DB;DP=71;FS=1.103;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=0;MQRankSum=0.860;QD=4.59;ReadPosRankSum=0.340;SOR=0.886;VQSLOD=-4.734e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:52,16:68:99:354,0,1641
-chr6	58778207	rs6588729	G	A	2273.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.00;AN=2;BaseQRankSum=1.676;ClippingRankSum=-1.397;DB;DP=65;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.24;MQ0=0;MQRankSum=0.950;NEGATIVE_TRAIN_SITE;QD=34.98;ReadPosRankSum=-1.341;SOR=0.236;VQSLOD=-1.078e+00;culprit=QD	GT:AD:DP:GQ:PL	1/1:1,61:62:99:2302,182,0
-chr6	58778244	rs6588730	A	T	2044.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.41;MQ0=0;QD=31.46;SOR=0.760;VQSLOD=4.48;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2073,180,0
-chr6	58778404	rs6588731	C	A	2347.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.80;MQ0=0;QD=32.04;SOR=0.808;VQSLOD=5.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,53:53:99:2376,160,0
-chr6	58778405	rs6588732	C	T	2392.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.66;MQ0=0;QD=27.48;SOR=0.770;VQSLOD=4.38;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2421,163,0
-chr6	58778412	rs6588733	T	C	2705.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.42;MQ0=0;QD=34.01;SOR=0.762;VQSLOD=5.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2734,184,0
-chr6	58778452	rs4928629	A	C	970.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.809;ClippingRankSum=-0.744;DB;DP=64;FS=5.099;MLEAC=1;MLEAF=0.500;MQ=55.54;MQ0=0;MQRankSum=2.130;POSITIVE_TRAIN_SITE;QD=15.17;ReadPosRankSum=1.163;SOR=1.249;VQSLOD=1.86;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:29,32:61:99:999,0,986
-chr6	58778456	.	G	T	154.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.779;ClippingRankSum=-0.534;DP=68;FS=2.839;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=1.216;NEGATIVE_TRAIN_SITE;QD=2.28;ReadPosRankSum=0.079;SOR=0.654;VQSLOD=-8.069e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:54,11:65:99:183,0,2074
-chr6	58778482	rs6588734	G	A	2628.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.61;MQ0=0;QD=31.77;SOR=0.906;VQSLOD=3.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2657,190,0
-chr6	58778519	rs4928633	A	G	847.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.545;ClippingRankSum=-1.803;DB;DP=75;FS=6.752;MLEAC=1;MLEAF=0.500;MQ=54.72;MQ0=0;MQRankSum=-1.213;QD=11.30;ReadPosRankSum=0.443;SOR=1.183;VQSLOD=-4.825e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:44,24:68:99:876,0,1700
-chr6	58778530	rs9647643	T	C	919.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=3.069;ClippingRankSum=-0.130;DB;DP=71;FS=8.855;MLEAC=1;MLEAF=0.500;MQ=54.76;MQ0=0;MQRankSum=-0.936;QD=12.95;ReadPosRankSum=-0.567;SOR=1.363;VQSLOD=-7.510e-02;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,26:64:99:948,0,1688
-chr6	58778531	rs9647644	A	C	922.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;ClippingRankSum=0.934;DB;DP=70;FS=8.966;MLEAC=1;MLEAF=0.500;MQ=54.68;MQ0=0;MQRankSum=-1.454;QD=13.18;ReadPosRankSum=-0.204;SOR=1.572;VQSLOD=-3.370e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,25:63:99:951,0,1651
-chr6	58778577	rs6588735	T	A	348.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;ClippingRankSum=0.432;DB;DP=70;FS=8.999;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=-0.934;NEGATIVE_TRAIN_SITE;QD=4.98;ReadPosRankSum=0.225;SOR=0.956;VQSLOD=-2.510e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:49,13:62:99:377,0,2028
-chr6	58778584	rs6588736	T	G	310.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.597;ClippingRankSum=0.859;DB;DP=67;FS=2.940;MLEAC=1;MLEAF=0.500;MQ=54.51;MQ0=0;MQRankSum=0.896;QD=4.64;ReadPosRankSum=0.545;SOR=0.275;VQSLOD=-1.432e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:48,12:60:99:339,0,2037
-chr6	58778664	rs112323615	T	G	597.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.932;ClippingRankSum=-0.755;DB;DP=68;FS=5.051;MLEAC=1;MLEAF=0.500;MQ=57.08;MQ0=0;MQRankSum=0.959;QD=8.79;ReadPosRankSum=-0.864;SOR=0.980;VQSLOD=-2.673e-01;culprit=QD	GT:AD:DP:GQ:PL	0/1:44,22:66:99:626,0,1333
-chr6	58778716	rs7453620	A	C	1189.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.027;ClippingRankSum=-0.970;DB;DP=79;FS=6.175;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-0.769;QD=15.06;ReadPosRankSum=-1.098;SOR=0.261;VQSLOD=0.195;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,39:75:99:1218,0,1070
-chr6	58778747	rs12214947	T	C	88.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;ClippingRankSum=-1.054;DB;DP=88;FS=4.622;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.705;NEGATIVE_TRAIN_SITE;QD=1.01;ReadPosRankSum=1.189;SOR=0.575;VQSLOD=-2.375e+00;culprit=QD	GT:AD:DP:GQ:PL	0/1:72,11:83:99:117,0,2437
-chr6	58778788	rs6651013	T	C	3397.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=99;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=34.32;SOR=0.976;VQSLOD=4.25;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,94:94:99:3426,282,0
-chr6	58778844	rs7452594	C	G	898.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=0.445;ClippingRankSum=-0.341;DB;DP=82;FS=12.217;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=0.289;QD=10.96;ReadPosRankSum=1.634;SOR=1.334;VQSLOD=-6.564e-01;culprit=FS	GT:AD:DP:GQ:PL	0/1:49,29:78:99:927,0,1649
-chr6	58778922	rs6651011	C	A	2529.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.00;AN=2;BaseQRankSum=1.683;ClippingRankSum=1.147;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.77;MQ0=0;MQRankSum=1.586;NEGATIVE_TRAIN_SITE;QD=34.19;ReadPosRankSum=-0.952;SOR=0.246;VQSLOD=-1.389e+00;culprit=FS	GT:AD:DP:GQ:PL	1/1:1,70:71:99:2558,204,0
-chr6	58778989	rs6651015	T	C	2986.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.71;MQ0=0;QD=37.21;SOR=0.722;VQSLOD=4.76;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,69:69:99:3015,208,0
-chr6	58779007	rs6651016	C	T	3187.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.13;MQ0=0;QD=33.52;SOR=0.836;VQSLOD=5.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,73:73:99:3216,223,0
-chr6	58779056	rs6937914	T	C	824.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.434;ClippingRankSum=0.011;DB;DP=75;FS=0.903;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-1.194;QD=11.00;ReadPosRankSum=0.535;SOR=0.535;VQSLOD=0.407;culprit=FS	GT:AD:DP:GQ:PL	0/1:41,31:72:99:853,0,1368
-chr6	58779089	rs4286808	C	A	635.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.994;ClippingRankSum=-1.111;DB;DP=63;FS=14.811;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.125;NEGATIVE_TRAIN_SITE;QD=10.09;ReadPosRankSum=0.169;SOR=1.477;VQSLOD=-1.459e+00;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,22:62:99:664,0,1572
-chr6	58779097	rs9500231	A	G	1804.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;ClippingRankSum=1.075;DB;DP=68;FS=2.521;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-0.173;QD=26.54;ReadPosRankSum=0.414;SOR=0.501;VQSLOD=-2.854e-01;culprit=DP	GT:AD:DP:GQ:PL	0/1:15,52:67:99:1833,0,403
-chr6	58779308	rs6651018	T	C	16.86	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;ClippingRankSum=-0.972;DB;DP=51;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=0;MQRankSum=-0.526;QD=0.33;ReadPosRankSum=0.430;SOR=0.783	GT:AD:DP:GQ:PL	0/1:42,6:48:45:45,0,1235
-chr6	58779328	rs6651019	A	G	1227.77	VQSRTrancheSNP99.00to99.90	AC=2;AF=1.00;AN=2;BaseQRankSum=0.974;ClippingRankSum=-1.310;DB;DP=39;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.52;MQ0=0;MQRankSum=0.772;QD=31.48;ReadPosRankSum=1.511;SOR=1.675;VQSLOD=0.201;culprit=FS	GT:AD:DP:GQ:PL	1/1:2,35:37:38:1256,38,0
-chr6	58779346	rs4376372	T	G	350.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.662;ClippingRankSum=-0.500;DB;DP=32;FS=2.071;MLEAC=1;MLEAF=0.500;MQ=39.86;MQ0=0;MQRankSum=0.460;QD=10.96;ReadPosRankSum=-0.500;SOR=1.292;VQSLOD=1.45;culprit=QD	GT:AD:DP:GQ:PL	0/1:18,13:31:99:379,0,605
-chr6	58779375	rs4250419	A	G	273.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.795;ClippingRankSum=-0.971;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.82;MQ0=0;MQRankSum=-0.442;QD=15.21;ReadPosRankSum=-1.589;SOR=1.781;VQSLOD=3.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,9:18:99:302,0,370
-chr6	58779376	rs6651020	C	T	736.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=30.93;MQ0=0;QD=27.25;SOR=4.294;VQSLOD=5.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,17:17:54:765,54,0
-chr6	58779409	rs4400241	T	C	160.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.793;ClippingRankSum=1.461;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.29;MQ0=0;MQRankSum=0.529;QD=13.40;ReadPosRankSum=1.788;SOR=1.371;VQSLOD=4.57;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,5:12:99:189,0,263
-chr6	58779468	rs6651021	A	G	83.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.90;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=4.64;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:28:112,0,28
-chr6	58779499	rs6651022	T	C	49.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.09;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:54:78,0,54
-chr6	61892431	rs4467815	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61909056	rs189688252	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61924395	rs74442497	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61924424	rs149028611	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61939361	rs76899121	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61967504	rs704487	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61967842	rs79961499	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	61984979	.	G	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:34:40,0,34
-chr6	62017935	rs1997843	T	C	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.50;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	62024599	rs1414786	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62027240	rs1074429	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62034435	rs115639864	C	T	36.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=0.406;QD=6.13;ReadPosRankSum=-0.406;SOR=0.693;VQSLOD=4.21;culprit=QD	GT:AD:DP:GQ:PL	0/1:3,3:6:65:65,0,104
-chr6	62084214	rs3908837	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62114785	rs7742522	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62183331	rs2092608	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62183845	rs35300708	C	CT	19.75	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.58;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:56,6,0
-chr6	62198757	rs6916640	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62208255	rs116736672	G	A	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.86;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	62217827	rs415716	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62220171	rs387256	A	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	62233173	rs214151	G	C	71.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.30;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.02;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-chr6	62236450	rs116060945	A	T	18.80	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.40;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:46,6,0
-chr6	62252108	rs4598053	C	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.68;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	62252188	rs67145854	GA	G	75.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	62269382	rs59519746	T	C	18.59	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:45,3,0
-chr6	62269405	rs56095991	G	T	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	62290945	rs140805963	G	A	44.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:31:73,0,31
-chr6	62294589	rs115452241	T	C	55.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.43;SOR=1.179;VQSLOD=6.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:83,9,0
-chr6	62316285	rs213776	A	C	47.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:67:76,0,67
-chr6	62329027	rs201975337	A	AT	15.82	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=7.91;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
-chr6	62390916	rs1204114	T	C	2091.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.71;SOR=0.765;VQSLOD=6.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,56:56:99:2120,168,0
-chr6	62413546	rs1204139	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62495041	rs78507898	T	A	20.78	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	62510310	rs1743448	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62515335	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62532253	rs571607	G	C	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	62582748	.	G	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:33:40,0,33
-chr6	62604848	.	T	TTC	69.25	PASS	AC=2;AF=1.00;AN=2;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.21;MQ0=0;QD=13.85;SOR=2.303;VQSLOD=5.37;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:9:106,9,0
-chr6	62650334	rs1114027	T	A	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	62674103	rs1192455	C	T	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	62674110	rs1192454	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	62686434	rs1192430	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62690574	rs1393669	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62706684	rs2102790	C	T	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=7.03;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	62708691	rs9453889	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	62757987	rs9346001	C	T	744.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.533;ClippingRankSum=0.028;DB;DP=52;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.661;POSITIVE_TRAIN_SITE;QD=14.32;ReadPosRankSum=1.294;SOR=0.546;VQSLOD=5.40;culprit=FS	GT:AD:DP:GQ:PL	0/1:28,24:52:99:773,0,900
-chr6	62886921	rs10455666	C	T	184.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.067;ClippingRankSum=-0.572;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=23.10;ReadPosRankSum=-0.572;SOR=1.863;VQSLOD=6.13;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,6:8:59:213,0,59
-chr6	62887031	rs9346218	C	T	1086.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.596;ClippingRankSum=1.848;DB;DP=62;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.846;POSITIVE_TRAIN_SITE;QD=17.53;ReadPosRankSum=-0.056;SOR=0.846;VQSLOD=5.07;culprit=FS	GT:AD:DP:GQ:PL	0/1:29,33:62:99:1115,0,921
-chr6	62887099	rs6921170	C	T	1783.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.393;ClippingRankSum=0.055;DB;DP=121;FS=0.706;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.039;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-0.465;SOR=0.841;VQSLOD=2.95;culprit=FS	GT:AD:DP:GQ:PL	0/1:60,60:120:99:1812,0,2047
-chr6	62995920	rs16883133	T	G	157.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-0.572;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=19.72;ReadPosRankSum=1.067;SOR=0.693;VQSLOD=6.06;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,6:8:55:186,0,55
-chr6	63018890	rs9354897	A	G	47.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.76;SOR=1.179;VQSLOD=7.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:75,9,0
-chr6	63022153	rs523967	G	A	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=9.05;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63022286	rs62414811	G	A	58.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.98;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:86,6,0
-chr6	63046505	rs508263	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63104500	rs2814661	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63116886	rs2452472	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63123748	rs2814696	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63139149	rs2452463	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63167529	rs2881136	G	A	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63171060	rs17381471	C	T	645.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.586;ClippingRankSum=-0.249;DB;DP=71;FS=9.277;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.188;POSITIVE_TRAIN_SITE;QD=9.10;ReadPosRankSum=-0.067;SOR=2.159;VQSLOD=0.690;culprit=QD	GT:AD:DP:GQ:PL	0/1:47,24:71:99:674,0,1531
-chr6	63171544	rs648165	A	T	113.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=-0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.380;POSITIVE_TRAIN_SITE;QD=18.96;ReadPosRankSum=1.380;SOR=1.329;VQSLOD=6.18;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:62:142,0,62
-chr6	63251196	rs2345983	C	T	109.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;ClippingRankSum=-0.550;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.550;SOR=0.941;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,4:7:90:138,0,90
-chr6	63257354	rs9446610	C	T	1142.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.489;ClippingRankSum=-0.017;DB;DP=75;FS=1.132;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.447;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=0.337;SOR=0.935;VQSLOD=3.19;culprit=FS	GT:AD:DP:GQ:PL	0/1:38,35:73:99:1171,0,1224
-chr6	63257971	rs6913632	T	C	1383.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.999;ClippingRankSum=0.127;DB;DP=63;FS=2.484;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=1.565;POSITIVE_TRAIN_SITE;QD=21.96;ReadPosRankSum=-0.367;SOR=0.382;VQSLOD=1.73;culprit=QD	GT:AD:DP:GQ:PL	0/1:19,44:63:99:1412,0,451
-chr6	63258233	rs11447029	C	CA	15.85	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.718;ClippingRankSum=-1.371;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.065;QD=0.99;ReadPosRankSum=0.588;SOR=0.160	GT:AD:DP:GQ:PL	0/1:11,4:15:53:53,0,220
-chr6	63290332	rs9351926	C	A	41.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:36:70,0,36
-chr6	63309881	rs73762312	G	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.61;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	63356605	rs4710365	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63357734	rs66885289	CTT	C	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.46;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	63370591	rs7776261	C	A	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.45;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	63370651	rs7761764	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63394799	rs4131720	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63426649	rs2752973	C	T	43.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.74;culprit=DP	GT:AD:DP:GQ:PL	0/1:1,2:3:32:72,0,32
-chr6	63480621	rs6937512	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63508240	rs4710370	A	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63508253	rs4710371	T	A	14.68	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.68;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0
-chr6	63520794	rs7746171	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63522176	rs9352169	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63567509	rs11961562	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63576005	rs55851245	C	G	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.14;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	63584587	rs12207161	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.52;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	63584592	rs12208504	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	63596076	rs7747071	G	A	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	63596112	rs4307155	C	T	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63607258	rs10943283	C	A	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	63727757	rs9343533	C	A	287.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.833;VQSLOD=6.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:316,24,0
-chr6	63730222	rs9352418	G	T	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.08;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	63730266	rs9343536	T	C	47.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.81;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	63733880	rs10943404	G	T	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.55;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63749658	rs6936280	A	G	59.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:87,6,0
-chr6	63749860	rs6941288	T	C	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.87;SOR=0.693;VQSLOD=4.12;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	63753907	rs12208886	A	G	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.60;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	63757242	.	G	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63775888	rs789964	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63785384	rs789954	G	A	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	63792401	rs1086295	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63863011	rs57238578	G	GGTTGTT	44.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	63874309	rs9343765	G	A	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.35;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	63874499	rs7747081	C	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	63885713	rs3059784	T	TTG	26.71	LowQual	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.71;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,1:1:6:63,6,0
-chr6	63885782	rs1020805	T	G	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	63902995	rs1847501	G	T	1552.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.223;ClippingRankSum=0.500;DB;DP=79;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.817;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.005;SOR=0.743;VQSLOD=4.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:34,45:79:99:1581,0,943
-chr6	63903354	rs16893840	G	T	550.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;ClippingRankSum=0.804;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=14.49;ReadPosRankSum=0.570;SOR=0.754;VQSLOD=5.91;culprit=FS	GT:AD:DP:GQ:PL	0/1:20,18:38:99:579,0,671
-chr6	63903377	rs6914331	G	A	1128.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.22;SOR=1.609;VQSLOD=5.16;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,28:28:84:1157,84,0
-chr6	63903384	rs2047899	G	T	382.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034;ClippingRankSum=-0.528;DB;DP=28;FS=1.690;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.080;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.345;SOR=0.269;VQSLOD=2.91;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:14,14:28:99:411,0,430
-chr6	63903574	rs142293404	GAAGGAGC	G	121.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=8;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-1.754;QD=15.22;ReadPosRankSum=0.000;SOR=2.494;VQSLOD=0.824;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:3,4:7:99:159,0,331
-chr6	63903606	rs116456502	G	A	133.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=0.000;DB;DP=6;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-1.380;POSITIVE_TRAIN_SITE;QD=22.29;ReadPosRankSum=1.231;SOR=3.258;VQSLOD=1.17;culprit=DP	GT:AD:DP:GQ:PL	0/1:2,4:6:99:162,0,243
-chr6	63921361	rs4710420	A	G	237.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.72;SOR=4.407;VQSLOD=7.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:266,24,0
-chr6	63921442	rs76273486	G	A	318.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.127;ClippingRankSum=-0.433;DB;DP=17;FS=3.274;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=2.261;POSITIVE_TRAIN_SITE;QD=18.75;ReadPosRankSum=1.299;SOR=1.981;VQSLOD=1.50;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:8,9:17:99:347,0,251
-chr6	63921456	rs79100944	G	A	493.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.628;ClippingRankSum=-0.102;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=1.740;QD=22.44;ReadPosRankSum=1.604;SOR=1.402;VQSLOD=0.390;culprit=FS	GT:AD:DP:GQ:PL	0/1:8,14:22:99:522,0,233
-chr6	63921924	rs9359357	A	G	278.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.409;ClippingRankSum=-1.184;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=-1.347;QD=14.67;ReadPosRankSum=1.266;SOR=1.609;VQSLOD=3.62;culprit=FS	GT:AD:DP:GQ:PL	0/1:10,9:19:99:307,0,291
-chr6	63933615	rs9352684	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63937797	rs12526013	T	C	105.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.116;ClippingRankSum=-0.735;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.41;MQ0=0;MQRankSum=-0.385;POSITIVE_TRAIN_SITE;QD=4.60;ReadPosRankSum=0.175;SOR=0.141;VQSLOD=3.69;culprit=QD	GT:AD:DP:GQ:PL	0/1:17,6:23:99:134,0,553
-chr6	63937863	rs3925806	T	C	119.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.720;POSITIVE_TRAIN_SITE;QD=19.96;ReadPosRankSum=0.720;SOR=0.368;VQSLOD=6.05;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,4:6:60:148,0,60
-chr6	63937916	rs3925805	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	63939795	rs1809272	T	C	2647.77	VQSRTrancheSNP99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.907;ClippingRankSum=0.336;DB;DP=202;FS=8.305;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=0;MQRankSum=-3.258;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.11;ReadPosRankSum=-0.632;SOR=0.350;VQSLOD=-4.749e-01;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:107,93:200:99:2676,0,3595
-chr6	63939829	rs1809271	A	T	8543.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=238;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.90;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=0.925;VQSLOD=3.77;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,237:237:99:8572,713,0
-chr6	63940061	rs4035417	A	G	1171.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=2.262;ClippingRankSum=-0.144;DB;DP=64;FS=5.367;MLEAC=1;MLEAF=0.500;MQ=51.76;MQ0=0;MQRankSum=-3.916;NEGATIVE_TRAIN_SITE;QD=18.31;ReadPosRankSum=1.606;SOR=0.207;VQSLOD=-1.900e+00;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:26,38:64:99:1200,0,790
-chr6	63940313	rs6905048	A	C	40.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-chr6	63969766	rs9352729	A	G	60.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:88,6,0
-chr6	63990648	rs35296992	A	G	956.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;ClippingRankSum=-0.057;DB;DP=88;FS=2.946;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=-0.678;POSITIVE_TRAIN_SITE;QD=10.87;ReadPosRankSum=-0.582;SOR=0.521;VQSLOD=1.69;culprit=QD	GT:AD:DP:GQ:PL	0/1:54,33:87:99:985,0,1782
-chr6	64126837	rs149978231	T	TAC	29.71	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=14.85;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:66,6,0
-chr6	64147016	rs144385019	AAGAAAGGGAGAAGGAAAAGAAAGAAAGG	A	85.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.12;MQ0=0;MQRankSum=-0.727;QD=21.43;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.01;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,3:4:99:123,0,203
-chr6	64150689	rs10755410	G	A	62.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.404;ClippingRankSum=-0.740;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.185;POSITIVE_TRAIN_SITE;QD=4.83;ReadPosRankSum=1.849;SOR=0.582;VQSLOD=4.90;culprit=QD	GT:AD:DP:GQ:PL	0/1:9,3:12:91:91,0,260
-chr6	64151093	rs9361767	A	G	149.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.572;ClippingRankSum=1.067;DB;DP=8;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=18.72;ReadPosRankSum=-1.589;SOR=0.105;VQSLOD=1.98;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:2,6:8:54:178,0,54
-chr6	64151771	rs9294215	C	G	107.78	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.731;ClippingRankSum=0.731;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=21.56;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,4:5:25:136,0,25
-chr6	64153691	rs2076874	G	A	46.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.47;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:74,6,0
-chr6	64189643	rs58741217	T	TCAAA	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	64190067	rs9443931	C	A	393.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.203;ClippingRankSum=-0.958;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.575;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-1.068;SOR=0.795;VQSLOD=5.07;culprit=FS	GT:AD:DP:GQ:PL	0/1:11,14:25:99:422,0,388
-chr6	64190278	rs2622276	A	T	386.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.855;ClippingRankSum=-0.153;DB;DP=29;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.065;POSITIVE_TRAIN_SITE;QD=13.34;ReadPosRankSum=-1.637;SOR=1.112;VQSLOD=2.78;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:14,15:29:99:415,0,464
-chr6	64190446	rs4299811	C	T	145.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.684;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.322;POSITIVE_TRAIN_SITE;QD=18.22;ReadPosRankSum=0.956;SOR=0.330;VQSLOD=6.88;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,5:8:87:174,0,87
-chr6	64190547	rs4557499	G	T	91.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=8.49;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:119,9,0
-chr6	64191578	rs10943822	A	T	30.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;ClippingRankSum=0.248;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.248;POSITIVE_TRAIN_SITE;QD=3.42;ReadPosRankSum=0.248;SOR=0.223;VQSLOD=4.86;culprit=QD	GT:AD:DP:GQ:PL	0/1:6,3:9:59:59,0,364
-chr6	64191586	rs10943823	T	C	73.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.566;ClippingRankSum=-0.382;DB;DP=11;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.566;POSITIVE_TRAIN_SITE;QD=6.71;ReadPosRankSum=0.715;SOR=0.132;VQSLOD=1.93;culprit=QD	GT:AD:DP:GQ:PL	0/1:8,3:11:99:102,0,417
-chr6	64191949	rs2800052	C	T	95.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=2.833;VQSLOD=7.66;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:123,9,0
-chr6	64209875	rs1744139	G	A	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.83;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	64209877	rs1779772	T	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.40;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	64221239	rs1744145	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64239405	rs1681942	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64258654	rs1744153	C	T	990.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.025;ClippingRankSum=1.004;DB;DP=65;FS=1.109;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=0.846;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=1.161;SOR=0.907;VQSLOD=3.16;culprit=FS	GT:AD:DP:GQ:PL	0/1:32,33:65:99:1019,0,1066
-chr6	64289938	.	AT	A	167.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.598;ClippingRankSum=0.045;DP=221;FS=3.210;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=0.356;QD=0.76;ReadPosRankSum=-0.923;SOR=0.391;VQSLOD=0.248;culprit=DP	GT:AD:DP:GQ:PL	0/1:132,35:167:99:205,0,2502
-chr6	64322622	rs34430878	CT	C	638.73	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.494;ClippingRankSum=-0.777;DB;DP=34;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;MQRankSum=1.255;QD=18.79;ReadPosRankSum=1.614;SOR=5.353;VQSLOD=3.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:1,28:29:60:676,60,0
-chr6	64322943	rs4583965	C	T	56.84	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=0.727;QD=4.74;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=3.30;culprit=QD	GT:AD:DP:GQ:PL	0/1:1,3:4:18:85,0,18
-chr6	64401952	rs200237690	CATT	C	919.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;ClippingRankSum=-0.006;DB;DP=77;FS=1.337;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-2.870;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-0.436;SOR=1.105;VQSLOD=1.29;culprit=MQRankSum	GT:AD:DP:GQ:PL	0/1:45,26:71:99:957,0,2148
-chr6	64419024	.	CT	C	25.74	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;ClippingRankSum=-2.457;DP=199;FS=4.601;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=0;MQRankSum=0.154;QD=0.13;ReadPosRankSum=-0.940;SOR=0.158	GT:AD:DP:GQ:PL	0/1:142,25:167:63:63,0,2866
-chr6	64472270	rs4710257	A	C	1520.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.301;ClippingRankSum=-0.541;DB;DP=75;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.155;POSITIVE_TRAIN_SITE;QD=20.28;ReadPosRankSum=-1.387;SOR=0.569;VQSLOD=4.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:32,43:75:99:1549,0,1031
-chr6	64498933	rs147210136	G	A	2218.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.180;ClippingRankSum=0.271;DB;DP=150;FS=9.259;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.467;POSITIVE_TRAIN_SITE;QD=14.79;ReadPosRankSum=1.950;SOR=0.286;VQSLOD=0.949;culprit=FS	GT:AD:DP:GQ:PL	0/1:75,74:149:99:2247,0,2088
-chr6	64513363	.	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64523255	.	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64574392	rs10638627	C	CTT	140.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.729;ClippingRankSum=0.729;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.98;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=-0.361;SOR=0.892;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:178,0,138
-chr6	64574396	rs10645485	T	TTC	100.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-0.361;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.361;QD=11.19;ReadPosRankSum=-0.361;SOR=0.527;VQSLOD=4.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,4:9:99:138,0,178
-chr6	64577850	rs321500	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64627882	rs677250	T	C	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.65;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	64686503	rs9362331	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64694354	rs4710457	C	T	3197.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;ClippingRankSum=1.756;DB;DP=194;FS=1.841;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.786;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=2.117;SOR=0.546;VQSLOD=2.30;culprit=DP	GT:AD:DP:GQ:PL	0/1:92,101:193:99:3226,0,2888
-chr6	64694560	rs1482457	G	A	2447.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.451;ClippingRankSum=0.305;DB;DP=164;FS=1.687;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.165;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=-0.002;SOR=0.497;VQSLOD=2.46;culprit=DP	GT:AD:DP:GQ:PL	0/1:89,74:163:99:2476,0,2876
-chr6	64694620	rs1482456	T	C	1132.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.667;ClippingRankSum=0.220;DB;DP=67;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.663;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.755;SOR=1.516;VQSLOD=4.16;culprit=FS	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1161,0,1169
-chr6	64708907	rs66502009	A	C	2569.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=3.193;ClippingRankSum=2.479;DB;DP=165;FS=4.658;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.156;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=1.406;SOR=1.162;VQSLOD=1.60;culprit=DP	GT:AD:DP:GQ:PL	0/1:81,84:165:99:2598,0,2412
-chr6	64752796	rs10944301	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64840987	rs3013170	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	64885636	rs4310034	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64949401	rs35507550	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64966049	rs2057165	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64968295	rs2057160	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	64995013	rs6917553	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65012918	rs9444712	T	C	558.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.612;ClippingRankSum=0.176;DB;DP=44;FS=1.724;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.129;POSITIVE_TRAIN_SITE;QD=12.70;ReadPosRankSum=-1.045;SOR=0.412;VQSLOD=2.58;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:22,22:44:99:587,0,721
-chr6	65013122	rs11753319	C	G	92.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368;ClippingRankSum=0.421;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=11.60;ReadPosRankSum=0.000;SOR=1.609;VQSLOD=6.06;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,4:8:99:121,0,142
-chr6	65013202	rs7739082	A	C	19.81	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=0.615;ClippingRankSum=-0.168;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.168;QD=1.04;ReadPosRankSum=0.056;SOR=0.495	GT:AD:DP:GQ:PL	0/1:16,3:19:48:48,0,530
-chr6	65021076	rs1922968	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65031098	rs1922975	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65037680	rs614395	G	C	38.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.956;ClippingRankSum=0.322;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=4.85;ReadPosRankSum=-0.322;SOR=0.818;VQSLOD=4.08;culprit=QD	GT:AD:DP:GQ:PL	0/1:5,3:8:67:67,0,135
-chr6	65051097	.	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65073876	rs671938	G	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.53;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
-chr6	65076921	.	A	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65084617	rs4518475	C	T	44.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=5.99;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:32:73,0,32
-chr6	65168481	rs35441646	C	CT	30.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.35;SOR=0.693;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-chr6	65204065	rs13211837	C	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65210797	rs34848022	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65218097	rs9362916	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65229459	rs13202092	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65236845	rs4710276	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65245271	.	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65274426	rs140935331	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65302877	rs75420781	A	T	134.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.198;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=-1.495;SOR=1.609;VQSLOD=5.71;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,5:7:61:163,0,61
-chr6	65302898	rs16895524	A	G	263.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.313;ClippingRankSum=1.381;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=0.533;POSITIVE_TRAIN_SITE;QD=20.29;ReadPosRankSum=0.817;SOR=1.179;VQSLOD=6.63;culprit=FS	GT:AD:DP:GQ:PL	0/1:5,8:13:99:292,0,150
-chr6	65302915	rs11331907	GA	G	124.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.088;ClippingRankSum=0.971;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQ0=0;MQRankSum=-1.678;POSITIVE_TRAIN_SITE;QD=6.93;ReadPosRankSum=2.208;SOR=0.693;VQSLOD=3.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:9,9:18:99:162,0,204
-chr6	65302987	rs139235690	ATATCT	A	997.73	VQSRTrancheINDEL99.00to99.90	AC=1;AF=0.500;AN=2;BaseQRankSum=2.195;ClippingRankSum=0.287;DB;DP=46;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.75;MQ0=0;MQRankSum=-3.550;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=3.163;SOR=0.571;VQSLOD=-9.260e-02;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:19,26:45:99:1035,0,709
-chr6	65303044	rs199667034	T	G	104.77	VQSRTrancheSNP99.90to100.00	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.183;ClippingRankSum=1.517;DB;DP=59;FS=83.060;MLEAC=1;MLEAF=0.500;MQ=52.39;MQ0=0;MQRankSum=0.300;QD=1.78;ReadPosRankSum=-1.257;SOR=5.992;VQSLOD=-1.136e+01;culprit=FS	GT:AD:DP:GQ:PL	0/1:40,19:59:99:133,0,1230
-chr6	65303100	rs17404123	T	C	1344.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.901;ClippingRankSum=-0.677;DB;DP=82;FS=0.838;MLEAC=1;MLEAF=0.500;MQ=54.84;MQ0=0;MQRankSum=-1.556;POSITIVE_TRAIN_SITE;QD=16.40;ReadPosRankSum=0.481;SOR=0.826;VQSLOD=2.46;culprit=FS	GT:AD:DP:GQ:PL	0/1:36,46:82:99:1373,0,1059
-chr6	65303381	rs17290119	T	C	46.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.60;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:31:75,0,31
-chr6	65305972	rs11759796	G	A	55.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:83,6,0
-chr6	65318362	rs9445030	C	T	61.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
-chr6	65341959	rs3028242	T	TATAAC	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	65365989	rs9445092	T	C	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	65369802	rs148392797	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65379468	rs1338822	A	T	12.05	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:32:40,0,32
-chr6	65423976	rs9452511	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65430160	rs9354068	C	T	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=5.09;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	65447951	rs70999169	A	AG	84.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.179;VQSLOD=8.62;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:121,9,0
-chr6	65473673	rs60268597	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65510460	rs34778588	CT	C	514.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;ClippingRankSum=-0.724;DB;DP=67;FS=1.771;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=-0.443;QD=7.68;ReadPosRankSum=1.520;SOR=1.167;VQSLOD=0.651;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:28,30:58:99:552,0,543
-chr6	65523111	rs9345532	A	C	67.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.322;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.920;POSITIVE_TRAIN_SITE;QD=8.47;ReadPosRankSum=-0.322;SOR=0.368;VQSLOD=5.25;culprit=QD	GT:AD:DP:GQ:PL	0/1:5,3:8:96:96,0,177
-chr6	65525121	rs1390272	C	T	133.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.271;ClippingRankSum=0.922;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=8.36;ReadPosRankSum=-1.139;SOR=0.412;VQSLOD=5.72;culprit=QD	GT:AD:DP:GQ:PL	0/1:10,6:16:99:162,0,313
-chr6	65533004	rs34714059	A	G	223.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;ClippingRankSum=-0.296;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.546;POSITIVE_TRAIN_SITE;QD=22.38;ReadPosRankSum=-0.296;SOR=1.609;VQSLOD=5.97;culprit=FS	GT:AD:DP:GQ:PL	0/1:3,7:10:91:252,0,91
-chr6	65545787	rs2172886	A	G	63.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.94;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
-chr6	65553444	rs2643788	A	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65569554	rs2146756	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65596759	rs7743515	G	A	2710.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.59;SOR=2.895;VQSLOD=5.93;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2739,226,0
-chr6	65611391	rs4710510	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65611814	rs57706332	T	C	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.90;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	65611832	rs142709378	A	C	128.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=6.74;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-chr6	65611952	rs59518422	T	TATTA	1930.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=3.767;VQSLOD=5.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1968,132,0
-chr6	65612302	rs75634595	A	G	3301.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.382;ClippingRankSum=-0.220;DB;DP=215;FS=1.153;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=0.451;POSITIVE_TRAIN_SITE;QD=15.36;ReadPosRankSum=2.299;SOR=0.598;VQSLOD=1.86;culprit=DP	GT:AD:DP:GQ:PL	0/1:108,107:215:99:3330,0,3121
-chr6	65622463	rs9294631	A	G	2159.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.924;ClippingRankSum=-0.947;DB;DP=134;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.365;POSITIVE_TRAIN_SITE;QD=16.12;ReadPosRankSum=2.546;SOR=0.693;VQSLOD=3.14;culprit=FS	GT:AD:DP:GQ:PL	0/1:70,64:134:99:2188,0,2257
-chr6	65622662	rs9445437	G	C	2121.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=5.294;ClippingRankSum=0.507;DB;DP=143;FS=5.248;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.124;POSITIVE_TRAIN_SITE;QD=14.84;ReadPosRankSum=1.501;SOR=1.441;VQSLOD=1.80;culprit=DP	GT:AD:DP:GQ:PL	0/1:81,62:143:99:2150,0,2628
-chr6	65622769	rs74484316	A	G	456.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.723;ClippingRankSum=-1.231;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.336;POSITIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.007;SOR=1.508;VQSLOD=5.31;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:485,0,229
-chr6	65622836	rs41516844	C	A	40.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=6.04;culprit=FS	GT:AD:DP:GQ:PL	0/1:2,2:4:69:69,0,76
-chr6	65632558	rs6455016	T	C	256.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=4.174;VQSLOD=6.56;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:285,21,0
-chr6	65678272	rs137904067	C	T	28.77	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;ClippingRankSum=-0.922;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.922;QD=4.11;ReadPosRankSum=0.922;SOR=0.223	GT:AD:DP:GQ:PL	0/1:5,2:7:57:57,0,186
-chr6	65715710	.	G	A	111.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-1.159;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.876;QD=12.42;ReadPosRankSum=-0.361;SOR=0.368;VQSLOD=4.52;culprit=FS	GT:AD:DP:GQ:PL	0/1:4,5:9:99:140,0,137
-chr6	65721195	rs7751922	G	A	84.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.33;MQ0=0;QD=28.09;SOR=2.833;VQSLOD=7.19;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:112,9,0
-chr6	65831684	rs9363336	G	A	64.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.84;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:92,9,0
-chr6	65995024	rs13214404	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	65999709	rs6455035	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66005609	rs34666704	AT	A	487.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.39;SOR=6.091;VQSLOD=6.41;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,20:20:60:525,60,0
-chr6	66005740	rs35045551	G	GA	1585.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;ClippingRankSum=-0.710;DB;DP=159;FS=1.564;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=9.97;ReadPosRankSum=1.276;SOR=0.921;VQSLOD=1.90;culprit=DP	GT:AD:DP:GQ:PL	0/1:79,74:153:99:1623,0,1557
-chr6	66005857	rs17411795	T	A	4088.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.317;ClippingRankSum=-0.640;DB;DP=271;FS=2.014;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.167;POSITIVE_TRAIN_SITE;QD=15.09;ReadPosRankSum=2.177;SOR=0.759;VQSLOD=1.94;culprit=DP	GT:AD:DP:GQ:PL	0/1:136,134:270:99:4117,0,4192
-chr6	66005888	rs9342464	C	T	4205.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=8.627;ClippingRankSum=0.069;DB;DP=251;FS=0.459;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.018;POSITIVE_TRAIN_SITE;QD=16.76;ReadPosRankSum=0.065;SOR=0.647;VQSLOD=1.79;culprit=FS	GT:AD:DP:GQ:PL	0/1:126,125:251:99:4234,0,3830
-chr6	66005970	rs9345601	G	A	3380.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.543;ClippingRankSum=-0.936;DB;DP=213;FS=2.475;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-1.449;POSITIVE_TRAIN_SITE;QD=15.87;ReadPosRankSum=1.107;SOR=0.516;VQSLOD=1.23;culprit=DP	GT:AD:DP:GQ:PL	0/1:103,109:212:99:3409,0,3103
-chr6	66006148	rs9342465	A	C	503.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.574;ClippingRankSum=0.709;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.485;POSITIVE_TRAIN_SITE;QD=23.99;ReadPosRankSum=0.485;SOR=1.508;VQSLOD=5.36;culprit=FS	GT:AD:DP:GQ:PL	0/1:7,14:21:99:532,0,220
-chr6	66013183	.	G	A	123.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.273;ClippingRankSum=-0.270;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.81;MQ0=0;MQRankSum=-0.039;QD=6.19;ReadPosRankSum=0.656;SOR=0.368;VQSLOD=3.44;culprit=QD	GT:AD:DP:GQ:PL	0/1:12,8:20:99:152,0,259
-chr6	66014572	rs75369872	A	G	25.75	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.00;MQ0=0;QD=12.88;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:53,6,0
-chr6	66018514	rs117228350	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66036758	rs13209408	G	A	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.23;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	66045077	rs1502965	C	T	2159.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.89;SOR=2.584;VQSLOD=6.42;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2188,183,0
-chr6	66045118	rs1502964	T	C	1434.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.16;SOR=6.091;VQSLOD=6.20;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1463,126,0
-chr6	66053835	rs1502963	T	G	2324.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.46;SOR=6.666;VQSLOD=7.17;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,56:56:99:2353,168,0
-chr6	66063513	rs1936439	G	A	3064.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.245;ClippingRankSum=-0.619;DB;DP=169;FS=3.043;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.296;POSITIVE_TRAIN_SITE;QD=18.13;ReadPosRankSum=1.339;SOR=0.465;VQSLOD=2.08;culprit=DP	GT:AD:DP:GQ:PL	0/1:65,104:169:99:3093,0,1991
-chr6	66063766	rs1936440	A	C	48.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.26;culprit=FS	GT:AD:DP:GQ:PL	0/1:1,2:3:33:77,0,33
-chr6	66066936	rs9294638	G	T	172.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.58;SOR=1.981;VQSLOD=6.69;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,5:5:15:201,15,0
-chr6	66067315	rs976727	A	C	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.30;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	66080074	rs9342469	G	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66112409	rs974110	A	G	2596.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.384;ClippingRankSum=-0.001;DB;DP=191;FS=0.540;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.531;POSITIVE_TRAIN_SITE;QD=13.60;ReadPosRankSum=3.882;SOR=0.763;VQSLOD=1.48;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/1:102,89:191:99:2625,0,3119
-chr6	66115281	rs34154043	G	GAAA	3245.73	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.314;ClippingRankSum=1.320;DB;DP=225;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=0.881;POSITIVE_TRAIN_SITE;QD=14.43;ReadPosRankSum=-2.390;SOR=0.705;VQSLOD=1.12;culprit=FS	GT:AD:DP:GQ:PL	0/1:99,90:189:99:3283,0,3862
-chr6	66141229	.	T	C	20.78	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:48,6,0
-chr6	66160560	rs9354246	A	G	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.68;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	66201364	rs9363379	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66204945	rs12193967	G	A	2169.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.754;ClippingRankSum=-0.093;DB;DP=128;FS=4.193;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.577;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=1.481;SOR=0.652;VQSLOD=2.12;culprit=DP	GT:AD:DP:GQ:PL	0/1:58,70:128:99:2198,0,1773
-chr6	66288101	rs150888347	A	AAT	77.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.36;MQ0=0;QD=25.75;SOR=1.179;VQSLOD=7.22;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:114,9,0
-chr6	66336763	rs6903740	T	C	42.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.26;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
-chr6	66336907	rs71736895	CCTTT	C	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66351345	rs6925080	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66375671	rs7757773	A	T	46.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.43;SOR=1.179;VQSLOD=7.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:74,9,0
-chr6	66379893	rs57880191	ACTC	A	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.36;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66379911	rs9283820	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.76;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66394859	rs1490125	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66409784	rs2812776	A	G	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.75;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66409789	rs2814115	T	C	62.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.59;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
-chr6	66411331	rs1490130	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66417384	rs9294647	G	T	52.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.92;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:80,6,0
-chr6	66418352	rs1490129	T	C	233.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.40;SOR=0.941;VQSLOD=6.77;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,7:7:21:262,21,0
-chr6	66418415	rs4609011	T	C	54.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.89;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
-chr6	66456318	rs2636129	T	C	49.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.31;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:77,6,0
-chr6	66456442	rs12526256	C	T	92.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=1.179;VQSLOD=8.78;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:120,9,0
-chr6	66471880	rs9453396	T	G	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66471897	rs9453397	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66471949	rs9445579	C	A	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.80;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	66524243	rs2802047	C	T	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66546565	rs4388276	G	A	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.99;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:76,6,0
-chr6	66547178	rs4392709	G	A	7412.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=208;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.34;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.53;SOR=0.857;VQSLOD=5.34;culprit=QD	GT:AD:DP:GQ:PL	1/1:0,208:208:99:7441,625,0
-chr6	66547322	rs9363455	T	G	5109.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=152;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=33.62;SOR=1.319;VQSLOD=4.64;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,152:152:99:5138,456,0
-chr6	66568995	rs6931427	G	A	62.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.21;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
-chr6	66596125	rs9283821	G	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66610269	rs9363483	A	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66710291	rs1484569	C	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66763069	rs1385225	A	G	57.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.11;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:85,6,0
-chr6	66763131	.	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66802808	rs4710310	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66803535	rs2881644	C	A	8655.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=238;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=0.789;VQSLOD=5.13;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,237:237:99:8684,713,0
-chr6	66803769	rs55951409	G	GGTTTCT	2785.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.86;MQ0=0;QD=27.53;SOR=0.960;VQSLOD=4.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2823,189,0
-chr6	66804609	rs147166458	GACTC	G	322.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.87;SOR=1.179;VQSLOD=5.97;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:24:360,24,0
-chr6	66804622	rs3925325	G	C	368.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.49;MQ0=0;QD=30.30;SOR=1.179;VQSLOD=5.58;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,8:8:27:397,27,0
-chr6	66804958	rs3030466	C	CCT	52.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.35;SOR=2.303;VQSLOD=8.57;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:89,6,0
-chr6	66807446	rs7738469	T	C	53.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:81,6,0
-chr6	66818604	rs3846808	T	C	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66829961	rs11287287	AG	A	38.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.71;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:75,6,0
-chr6	66836869	rs13217074	A	G	56.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=7.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:84,6,0
-chr6	66849936	rs866452	T	A	21.77	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-chr6	66871532	rs138893096	C	CAAAG	53.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:90,6,0
diff --git a/setup.py b/setup.py
index 18f99ff..a221c56 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
 from setuptools import setup
 from os import path
 
-VERSION = (1, 0, '0b1')
+VERSION = (2, 0, '0b1')
 __version__ = VERSION
 __versionstr__ = '.'.join(map(str, VERSION))
 
@@ -13,6 +13,7 @@
     packages=['variantapi'],
     url='https://github.com/saphetor/variant-api-client-python',
     license='Apache License, Version 2.0',
+    package_data={'': ['annotate_vcf.py', 'run.py']},
     author='Saphetor',
     author_email='support@saphetor.com',
     description='A basic python api client implementation for https://api.varsome.com',
@@ -21,12 +22,12 @@
         'Intended Audience :: Developers',
         'Operating System :: OS Independent',
         'License :: OSI Approved :: Apache License',
-        'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.2',
         'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
     ],
     install_requires=[
         'requests>=2.0.0, <3.0.0',
diff --git a/variantapi/client.py b/variantapi/client.py
index 3adbc84..18ecd6d 100644
--- a/variantapi/client.py
+++ b/variantapi/client.py
@@ -1,11 +1,11 @@
 import logging
-
+import asyncio
+import concurrent.futures
+import re
+import os
 import requests
 from requests.exceptions import HTTPError, Timeout, ConnectionError, RequestException
 
-# Set DEBUG variable to affect certain parameters
-_debug = False
-
 
 class VariantApiException(Exception):
     ERROR_CODES = {
@@ -36,12 +36,22 @@ def __repr__(self):
 
 
 class VariantAPIClientBase(object):
-    _api_url = 'https://api.varsome.com' if not _debug else 'https://dev-api.varsome.com'
+    _api_url = 'https://api.varsome.com'
     _accepted_methods = ('GET', 'POST')
 
-    def __init__(self, api_key=None):
+    def __init__(self, api_key=None, logger=None):
+        if logger is None:
+            BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+            logger = logging.getLogger(__name__)
+            logger.setLevel(logging.DEBUG)
+            formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+            ch = logging.FileHandler(os.path.join(BASE_DIR, 'output.log'))
+            ch.setLevel(logging.DEBUG)
+            ch.setFormatter(formatter)
+            logger.addHandler(ch)
+        self.logger = logger
         self.api_key = api_key
-        self._headers = {'Accept': 'application/json'}
+        self._headers = {'Accept': 'application/json', 'user-agent': 'VarSomeApiClientPython/2.0'}
         if self.api_key is not None:
             self._headers['Authorization'] = "Token " + self.api_key
         self.session = requests.Session()
@@ -52,72 +62,115 @@ def _make_request(self, path, method="GET", params=None, json_data=None):
             raise VariantApiException('', "Unsupported method %s" % method)
         try:
             if method == "GET":
-                r = self.session.get(self._api_url + path, params=params)
+                r = self.session.get(self._api_url + path, params=params, stream=True)
             if method == "POST":
+                if json_data is None:
+                    raise RuntimeError("You need to provide a post request body")
                 r = self.session.post(self._api_url + path, params=params, json=json_data,
-                                      headers={'Content-Type': 'application/json'} if json_data is not None else None)
-                logging.debug('Time between request and response %s' % r.elapsed)
-                logging.debug('Content length %s' % len(r.content))
-            if r.status_code in VariantApiException.ERROR_CODES:
-                raise VariantApiException(
-                    r.status_code,
-                    r.json()['detail']
-                    if r.headers['Content-Type'] == "application/json" else None)
+                                      headers={'Content-Type': 'application/json'}, stream=True)
+                self.logger.info('Time between request and response %s' % r.elapsed)
+                self.logger.info('Content length %s' % len(r.content))
+            r.raise_for_status()
             return r
         except HTTPError as e:
+            response = e.response
+            if response.status_code in VariantApiException.ERROR_CODES:
+                error_message = "Unexpected error"
+                if r.headers['Content-Type'] == "application/json":
+                    error_message = response.json().get("detail", None)
+                raise VariantApiException(response.status_code, error_message)
             raise VariantApiException('', "Unknown http error %s" % e)
         except Timeout as e:
             raise VariantApiException('', "Request timed out %s" % e)
         except ConnectionError as e:
             raise VariantApiException('', "Connection failure or connection refused %s" % e)
         except RequestException as e:
-            raise VariantApiException('', "Unknown error %s" % e.response)
+            raise VariantApiException('', "Unknown error %s" % e)
 
     def get(self, path, params=None):
         response = self._make_request(path, "GET", params=params)
         return response.json()
 
-    def post(self, path, params=None, json_data=None):
-        response = self._make_request(path, "POST", params=params, json_data=json_data)
-        return response.json()
+    def post(self, path, params=None, json_data=None, raise_exceptions=False):
+        # handle api errors in batch requests.
+        try:
+            response = self._make_request(path, "POST", params=params, json_data=json_data)
+            return response.json()
+        except VariantApiException as e:
+            if raise_exceptions:
+                raise e
+            self.logger.error(e)
+            return {'error': str(e)}
 
 
 class VariantAPIClient(VariantAPIClientBase):
-    schema_lookup_path = "/lookup/schema/"
-    lookup_path = "/lookup/%s/%s"
+    schema_lookup_path = "/lookup/schema"
+    lookup_path = "/lookup/%s"
+    ref_genome_lookup_path = lookup_path + "/%s"
     batch_lookup_path = "/lookup/batch/%s"
 
     def __init__(self, api_key=None, max_variants_per_batch=200):
         super(VariantAPIClient, self).__init__(api_key)
         self.max_variants_per_batch = max_variants_per_batch
 
+    def query_is_variant_id(self, query):
+        """
+        Query may be a variat identifier developed by Saphetor
+        :param query:
+        :return:
+        """
+        return re.search(r'^\d{20}$', str(query))
+
     def schema(self):
         return self.get(self.schema_lookup_path)
 
-    def lookup(self, query, params=None, ref_genome='hg19'):
+    def lookup(self, query, params=None, ref_genome=None):
         """
 
         :param query: variant representation
         :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation
         of https://api.varsome.com for examples
-        :param ref_genome: reference genome (hg19 or hg38)
+        :param ref_genome: reference genome (hg19 or hg38 or None) default for requests with no ref genome is hg19
         :return:dictionary of annotations. refer to https://api.varsome.com/lookup/schema for dictionary properties
         """
-        return self.get(self.lookup_path % (query, ref_genome), params=params)
+        url = self.lookup_path % query
+        if ref_genome is not None and not self.query_is_variant_id(query):
+            url = self.ref_genome_lookup_path % (query, ref_genome)
+        return self.get(url, params=params)
 
-    def batch_lookup(self, variants, params=None, ref_genome='hg19'):
+    def batch_lookup(self, variants, params=None, ref_genome='hg19', max_threads=3, raise_exceptions=False):
         """
 
         :param variants: list of variant representations
         :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation
         of https://api.varsome.com for examples
         :param ref_genome: reference genome (hg19 or hg38)
+        :param max_threads: how many concurrent requests to make
+        (max_variants_per_batch has to be less than len(variants) param to have any effect)
+        :raise_exceptions: If a post request should raise an exception True, thus terminating the whole process or if it
+        should proceed to let the process continue
         :return: list of dictionaries with annotations per variant refer to https://api.varsome.com/lookup/schema
         for dictionary properties
         """
         results = []
-        for queries in [variants[x:x + self.max_variants_per_batch] for x in range(0, len(variants),
-                                                                                   self.max_variants_per_batch)]:
-            data = self.post(self.batch_lookup_path % ref_genome, params=params, json_data={'variants': queries})
-            results.extend(data)
+
+        async def batch(executor):
+            loop = asyncio.get_event_loop()
+            futures = [
+                loop.run_in_executor(
+                    executor,
+                    self.post,
+                    self.batch_lookup_path % ref_genome, params, {'variants': queries}, raise_exceptions
+                )
+                for queries in [variants[x:x + self.max_variants_per_batch] for x in range(0, len(variants),
+                                                                                           self.max_variants_per_batch)]
+            ]
+            for response in await asyncio.gather(*futures):
+                results.extend(response)
+        # Create a limited thread pool.
+        executor = concurrent.futures.ThreadPoolExecutor(
+                max_workers=max_threads,
+        )
+        loop = asyncio.get_event_loop()
+        loop.run_until_complete(batch(executor))
         return results
diff --git a/variantapi/models/variant.py b/variantapi/models/variant.py
index a943884..e200554 100644
--- a/variantapi/models/variant.py
+++ b/variantapi/models/variant.py
@@ -1,8 +1,14 @@
+from .fields import DictField
 from .elements import *
 
 __author__ = "ckopanos"
 
 class AnnotatedVariant(models.Base):
+    """
+    Base variant result definition model
+    Most fields are defined as list fields, even though they contain a single list item
+    This is due to the fact that VarSome API can return both current and old versions of databases
+    """
 
     chromosome = fields.StringField(help_text="Chromosome")
     alt = fields.StringField(help_text="ALT Sequence", required=False, nullable=True)
@@ -39,9 +45,44 @@ class AnnotatedVariant(models.Base):
 
     @property
     def genes(self):
+        genes = []
+        genes.extend(self.refseq_genes)
+        genes.extend(self.ensembl_genes)
+        return list(set(genes))
+
+    @property
+    def refseq_genes(self):
         genes = []
         for transcript in self.refseq_transcripts:
-            for item in transcript.items:
-                if item.gene_symbol:
-                    genes.append(item.gene_symbol)
-        return genes
\ No newline at end of file
+            genes.extend([item.gene_symbol for item in transcript.items if item.gene_symbol])
+        return genes
+
+    @property
+    def ensembl_genes(self):
+        genes = []
+        for transcript in self.ensembl_transcripts:
+            genes.extend([item.gene_symbol for item in transcript.items if item.gene_symbol])
+        return genes
+
+    @property
+    def rs_ids(self):
+        rs_ids = []
+        for dbnsp_entry in self.ncbi_dbsnp:
+            rs_ids.extend(dbnsp_entry.rsid)
+        return ["rs%s" % rs_id for rs_id in rs_ids]
+
+    @property
+    def gnomad_exomes_af(self):
+        """
+        Returns the gnomad exomes af value.
+        :return:
+        """
+        af = [gnomad_exomes.af for gnomad_exomes in self.gnomad_exomes]
+        return af[0] if af else None
+
+    @property
+    def gnomad_genomes_af(self):
+        af = [gnomad_genomes.af for gnomad_genomes in self.gnomad_genomes]
+        return af[0] if af else None
+
+
diff --git a/variantapi/vcf.py b/variantapi/vcf.py
index ecd8e68..4352c0a 100644
--- a/variantapi/vcf.py
+++ b/variantapi/vcf.py
@@ -1,8 +1,9 @@
+import os
+import time
+import vcf
 from collections import OrderedDict
-
-from variantapi.client import VariantAPIClient, VariantApiException
-import os, vcf
-
+from vcf.parser import _Info
+from variantapi.client import VariantAPIClient
 from variantapi.models.variant import AnnotatedVariant
 
 __author__ = "ckopanos"
@@ -14,39 +15,106 @@ class VCFAnnotator(VariantAPIClient):
     """
 
     def __init__(self, api_key=None,
-                 max_variants_per_batch=200, ref_genome='hg19', get_parametes=None):
+                 max_variants_per_batch=1000, ref_genome='hg19', get_parameters=None, max_threads=None):
         super().__init__(api_key, max_variants_per_batch)
         self.ref_genome = ref_genome
-        self.get_parameters = get_parametes
+        self.get_parameters = get_parameters
+        self.total_varialts = 0
+        self.filtered_out_variants = 0
+        self.variants_with_errors = 0
+        self.max_threads = max_threads or 1
+        if self.max_variants_per_batch > 3000 and self.max_threads > 1:
+            self.logger.warning("Having more than 1 thread with more than 3000 variants per batch may not be optimal")
+
+    def _process_request(self, input_batch):
+        start = time.time()
+        api_results = self.batch_lookup(list(input_batch.keys()), params=self.get_parameters,
+                                        ref_genome=self.ref_genome, max_threads=self.max_threads)
+        duration = time.time() - start
+        self.logger.info('Annotated %s variants in %s' % (len(input_batch), duration))
+        for i, requested_variant in enumerate(input_batch.keys()):
+            try:
+                results = api_results[i]
+                record = input_batch[requested_variant]
+                if results:
+                    if 'filtered_out' in results:
+                        self.logger.info(results['filtered_out'])
+                        self.filtered_out_variants += 1
+                        continue
+                    if 'error' in results:
+                        self.logger.error(results['error'])
+                        self.variants_with_errors += 1
+                        continue
+                    if 'variant_id' in results:
+                        variant_result = AnnotatedVariant(**results)
+                        record = self.annotate_record(record, variant_result)
+                        self.vcf_writer.write_record(record)
+                    else:
+                        self.logger.error(results)
+                        self.variants_with_errors += 1
+            except Exception as e:
+                self.logger.error(e)
+                self.variants_with_errors += 1
+                pass  # log an exception..
+
+    def annotate_record(self, record, variant_result):
+        """
+        Method to annotate a record. You should override this with your own implementation
+        to include variant result properties you want in your output vcf
+        :param record: vcf record object
+        :param variant_result: AnnotatedVariant object
+        :return: annotated record object
+        """
+        record.INFO['variant_id'] = variant_result.variant_id
+        record.INFO['gene'] = ",".join(variant_result.genes)
+        record.INFO['gnomad_exomes_AF'] = variant_result.gnomad_exomes_af
+        record.INFO['gnomad_genomes_AF'] = variant_result.gnomad_exomes_af
+        record.ALT = variant_result.alt
+        record.POS = variant_result.pos
+        record.ID = ";".join(variant_result.rs_ids) or "."
+        return record
+
+    def add_vcf_header_info(self, vcf_writer):
+        """
+        Adds vcf INFO headers for the annotated values provided
+        This is just a base method you need to override in your own implementation
+        depending on the annotations added through the annotate_record method
+        :param vcf_writer: vcf writer object
+        :return:
+        """
+        vcf_writer.infos['variant_id'] = _Info('variant_id', 1, 'Integer', 'Saphetor variant identifier', None, None)
+        vcf_writer.infos['gene'] = _Info('gene', '.', 'String', 'Genes related to this variant', None, None)
+        vcf_writer.infos['gnomad_exomes_AF'] = _Info('gnomad_exomes_AF', '.', 'Float',
+                                                     'GnomAD exomes allele frequency value', None, None)
+        vcf_writer.infos['gnomad_genomes_AF'] = _Info('gnomad_genomes_AF', '.', 'Float',
+                                                      'GnomAD genomes allele frequency value', None, None)
 
     def annotate(self, input_vcf_file, output_vcf_file=None):
+        annotations_start = time.time()
         if not os.path.isfile(input_vcf_file):
             raise FileNotFoundError('%s does not exist' % input_vcf_file)
         if output_vcf_file is None:
             output_vcf_file = "%s.annotated.vcf" % input_vcf_file
-        vcf_reader = vcf.Reader(filename=input_vcf_file)
-        vcf_writer = vcf.Writer(open(output_vcf_file, 'w'), vcf_reader)
+        vcf_reader = vcf.Reader(filename=input_vcf_file, strict_whitespace=True)
+        self.vcf_writer = vcf.Writer(open(output_vcf_file, 'w'), vcf_reader)
+        self.add_vcf_header_info(self.vcf_writer)
         input_batch = OrderedDict()
+        # this will keep the request queue large enough so that parallel requests will not stop executing
+        batch_limit = self.max_variants_per_batch * self.max_threads * 2
         for record in vcf_reader:
             for alt_seq in record.ALT:
                 requested_variant = "%s:%s:%s:%s" % (record.CHROM, record.POS, record.REF or "", alt_seq or "")
                 input_batch[requested_variant] = record
-            if len(input_batch) < self.max_variants_per_batch:
+                self.total_varialts += 1
+            if len(input_batch) < batch_limit:
                 continue
-            api_results = self.batch_lookup(list(input_batch.keys()), params=self.get_parameters, ref_genome=self.ref_genome)
-            for i, requested_variant in enumerate(input_batch.keys()):
-                try:
-                    variant_result = AnnotatedVariant(**api_results[i])
-                    record = input_batch[requested_variant]
-                    record.INFO['VARIANT_ID'] = variant_result.variant_id
-                    record.INFO['GENE'] = ",".join(variant_result.genes)
-                except Exception as e:
-                    print(api_results[i]['variant_id'], e)
-                    pass
-                vcf_writer.write_record(record)
-
-
+            self._process_request(input_batch)
             # reset input batch
             input_batch = OrderedDict()
-
-
+            # we may have some variants remaining if input batch is less than batch size
+        if len(input_batch) > 0:
+            self._process_request(input_batch)
+        self.logger.info("Annotating %s variants in %s. "
+                         "Filtered out %s. "
+                         "Errors %s" % (self.total_varialts, time.time() - annotations_start,
+                                        self.filtered_out_variants, self.variants_with_errors))

From d83f6a60fa863d8ae3765ca3c7b5af8f6cd6c1a0 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Wed, 10 Jan 2018 15:00:59 +0200
Subject: [PATCH 04/31] Modified run.py to accept input and output files. Fix
 in client.py for forgotten static method

---
 run.py               | 72 ++++++++++++++++++++++++++++++++++----------
 variantapi/client.py |  2 +-
 2 files changed, 57 insertions(+), 17 deletions(-)

diff --git a/run.py b/run.py
index 51236dc..b4a8c1a 100755
--- a/run.py
+++ b/run.py
@@ -22,12 +22,12 @@ def annotate_variant(argv):
                         help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
                         type=str, metavar='Request Params', required=False, nargs='+')
     parser.add_argument('-i',
-                        help='Path to csv file with variants. It should include one variant per line. Don\'t use it '
+                        help='Path to text file with variants. It should include one variant per line. Don\'t use it '
                              'together with the -q option',
-                        type=str, metavar='CSV File', required=False)
+                        type=str, metavar='Text/CSV File one line per variant', required=False)
     parser.add_argument('-o',
                         help='Path to output file to store variant annotations',
-                        type=str, metavar='CSV File', required=False)
+                        type=str, metavar='Output File with json entries', required=False)
     args = parser.parse_args()
     api_key = args.k
     query = args.q
@@ -35,30 +35,70 @@ def annotate_variant(argv):
     input_file = args.i
     output_file = args.o
     if query and input_file:
-        sys.stderr.write("Don't specify -i and -q options together. Use only one of them")
+        sys.stderr.write("Don't specify -i and -q options together. Use only one of them\n")
         sys.exit(1)
     if not query and not input_file:
-        sys.stderr.write("Please either specify -i or -q options")
+        sys.stderr.write("Please either specify -i or -q options\n")
         sys.exit(1)
     if input_file and not os.path.exists(input_file):
-        sys.stderr.write('File %s does not exist' % input_file)
+        sys.stderr.write('File %s does not exist\n' % input_file)
         sys.exit(1)
-    if output_file and not os.path.exists(output_file):
-        sys.stderr.write('File %s already exists' % input_file)
+    if output_file and os.path.exists(output_file):
+        sys.stderr.write('File %s already exists\n' % output_file)
         sys.exit(1)
     request_parameters = None
     if args.p:
         request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
     api = VariantAPIClient(api_key)
-
-    if len(query) == 1:
-        result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome)
+    if query:
+        if len(query) == 1:
+            result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome)
+        else:
+            if api_key is None:
+                sys.exit("You need to pass an api key to perform batch requests")
+            result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome)
+        sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+        sys.stdout.write("\n")
+        sys.exit(0)
+    with open(input_file) as f:
+        variants = f.read().splitlines()
+    if variants:
+        if len(variants) > 1000:
+            sys.stdout.write('Too many variants.. Consider using annotate_vcf instead\n')
+            sys.stdout.flush()
+        write_f = None
+        if output_file:
+            write_f = open(output_file, 'w')
+        try:
+            if api_key is None:
+                results = []
+                for variant in variants:
+                    result = api.lookup(variant, params=request_parameters, ref_genome=ref_genome)
+                    if not result:
+                        result = {'error': 'Could not fetch annotations for %s' % variant}
+                    results.append(result)
+                if write_f is not None:
+                    json.dump(results, write_f, indent=4, sort_keys=True)
+                else:
+                    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+                    sys.stdout.write("\n")
+            else:
+                result = api.batch_lookup(variants, params=request_parameters, ref_genome=ref_genome)
+                if write_f is not None:
+                    json.dump(result, write_f, indent=4, sort_keys=True)
+                else:
+                    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+                    sys.stdout.write("\n")
+        except Exception as e:
+            # several things might occur. This is to broad, but lets not keep open file handles
+            sys.stderr.write(str(e))
+            sys.stderr.write("\n")
+            if write_f is not None:
+                write_f.close()
+            sys.exit(1)
     else:
-        if api_key is None:
-            sys.exit("You need to pass an api key to perform batch requests")
-        result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome)
-    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
-    sys.stdout.write("\n")
+        sys.stderr.write('No variants found in file %s\n' % input_file)
+        sys.exit(1)
 
 
 if __name__ == "__main__":
diff --git a/variantapi/client.py b/variantapi/client.py
index 7a89e68..46e9286 100755
--- a/variantapi/client.py
+++ b/variantapi/client.py
@@ -113,7 +113,7 @@ def __init__(self, api_key=None, max_variants_per_batch=200):
         super(VariantAPIClient, self).__init__(api_key)
         self.max_variants_per_batch = max_variants_per_batch
 
-    @staticmethod
+
     def query_is_variant_id(self, query):
         """
         Query may be a variat identifier developed by Saphetor

From 7f7ae6987f1dbe1801715d8467ac76c440d6d807 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Wed, 10 Jan 2018 19:08:21 +0200
Subject: [PATCH 05/31] Transformed setup.py so that scripts former run.py and
 annotate_vcf.py are installed under the venv bin directory so that their
 always within the current PATH

---
 .gitignore                         |   1 -
 scripts/variantapi_annotate_vcf.py |  41 +++++++++++
 scripts/variantapi_run.py          | 105 +++++++++++++++++++++++++++++
 3 files changed, 146 insertions(+), 1 deletion(-)
 create mode 100755 scripts/variantapi_annotate_vcf.py
 create mode 100755 scripts/variantapi_run.py

diff --git a/.gitignore b/.gitignore
index f314e58..18a0714 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,7 +8,6 @@
 [Ll]ib
 [Ll]ib64
 [Ll]ocal
-[Ss]cripts
 pyvenv.cfg
 .venv
 pip-selfcheck.json
diff --git a/scripts/variantapi_annotate_vcf.py b/scripts/variantapi_annotate_vcf.py
new file mode 100755
index 0000000..e0fe770
--- /dev/null
+++ b/scripts/variantapi_annotate_vcf.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+import argparse
+import sys
+
+from variantapi.vcf import VCFAnnotator
+
+__author__ = 'ckopanos'
+
+
+def annotate_vcf(argv):
+    parser = argparse.ArgumentParser(description='VCF Annotator command line')
+    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True)
+    parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
+                        required=False, default='hg19')
+    parser.add_argument('-i',
+                        help='Path to vcf file',
+                        type=str, metavar='Input VCF File', required=True)
+    parser.add_argument('-o',
+                        help='Path to output vcf file',
+                        type=str, metavar='Output VCF File', required=False)
+    parser.add_argument('-p',
+                        help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
+                        type=str, metavar='Request Params', required=False, nargs='+')
+    parser.add_argument('-t', help='Run vcf annotator using x threads', type=int, default=3, required=False,
+                        metavar='Number of threads')
+    args = parser.parse_args()
+    api_key = args.k
+    vcf_file = args.i
+    output_vcf_file = args.o
+    ref_genome = args.g
+    num_threads = args.t
+    request_parameters = None
+    if args.p:
+        request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
+    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parameters=request_parameters,
+                                 max_threads=num_threads)
+    vcf_annotator.annotate(vcf_file, output_vcf_file)
+
+
+if __name__ == "__main__":
+    annotate_vcf(sys.argv[1:])
diff --git a/scripts/variantapi_run.py b/scripts/variantapi_run.py
new file mode 100755
index 0000000..b4a8c1a
--- /dev/null
+++ b/scripts/variantapi_run.py
@@ -0,0 +1,105 @@
+#!/usr/bin/env python
+import argparse
+import json
+import sys
+import os
+
+from variantapi.client import VariantAPIClient
+
+__author__ = 'ckopanos'
+
+
+def annotate_variant(argv):
+    parser = argparse.ArgumentParser(description='Sample Variant API calls')
+    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
+    parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
+                        required=False, default='hg19')
+    parser.add_argument('-q',
+                        help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request '
+                             'e.g. chr19:20082943:1:G rs113488022. Don\'t use it together with the -i option',
+                        type=str, metavar='Query', required=False, nargs='+')
+    parser.add_argument('-p',
+                        help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
+                        type=str, metavar='Request Params', required=False, nargs='+')
+    parser.add_argument('-i',
+                        help='Path to text file with variants. It should include one variant per line. Don\'t use it '
+                             'together with the -q option',
+                        type=str, metavar='Text/CSV File one line per variant', required=False)
+    parser.add_argument('-o',
+                        help='Path to output file to store variant annotations',
+                        type=str, metavar='Output File with json entries', required=False)
+    args = parser.parse_args()
+    api_key = args.k
+    query = args.q
+    ref_genome = args.g
+    input_file = args.i
+    output_file = args.o
+    if query and input_file:
+        sys.stderr.write("Don't specify -i and -q options together. Use only one of them\n")
+        sys.exit(1)
+    if not query and not input_file:
+        sys.stderr.write("Please either specify -i or -q options\n")
+        sys.exit(1)
+    if input_file and not os.path.exists(input_file):
+        sys.stderr.write('File %s does not exist\n' % input_file)
+        sys.exit(1)
+    if output_file and os.path.exists(output_file):
+        sys.stderr.write('File %s already exists\n' % output_file)
+        sys.exit(1)
+    request_parameters = None
+    if args.p:
+        request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
+    api = VariantAPIClient(api_key)
+    if query:
+        if len(query) == 1:
+            result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome)
+        else:
+            if api_key is None:
+                sys.exit("You need to pass an api key to perform batch requests")
+            result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome)
+        sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+        sys.stdout.write("\n")
+        sys.exit(0)
+    with open(input_file) as f:
+        variants = f.read().splitlines()
+    if variants:
+        if len(variants) > 1000:
+            sys.stdout.write('Too many variants.. Consider using annotate_vcf instead\n')
+            sys.stdout.flush()
+        write_f = None
+        if output_file:
+            write_f = open(output_file, 'w')
+        try:
+            if api_key is None:
+                results = []
+                for variant in variants:
+                    result = api.lookup(variant, params=request_parameters, ref_genome=ref_genome)
+                    if not result:
+                        result = {'error': 'Could not fetch annotations for %s' % variant}
+                    results.append(result)
+                if write_f is not None:
+                    json.dump(results, write_f, indent=4, sort_keys=True)
+                else:
+                    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+                    sys.stdout.write("\n")
+            else:
+                result = api.batch_lookup(variants, params=request_parameters, ref_genome=ref_genome)
+                if write_f is not None:
+                    json.dump(result, write_f, indent=4, sort_keys=True)
+                else:
+                    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+                    sys.stdout.write("\n")
+        except Exception as e:
+            # several things might occur. This is to broad, but lets not keep open file handles
+            sys.stderr.write(str(e))
+            sys.stderr.write("\n")
+            if write_f is not None:
+                write_f.close()
+            sys.exit(1)
+    else:
+        sys.stderr.write('No variants found in file %s\n' % input_file)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    annotate_variant(sys.argv[1:])

From eaf1e36c6e909ee210c0195bd1f6ea79d758a3c2 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Wed, 10 Jan 2018 19:13:05 +0200
Subject: [PATCH 06/31] Transformed setup.py so that scripts former run.py and
 annotate_vcf.py are installed under the venv bin directory so that their
 always within the current PATH

---
 MANIFEST.in                    |   5 +-
 README.md                      |  29 +++++----
 annotate_vcf.py                |  41 -------------
 run.py                         | 105 ---------------------------------
 setup.py                       |  16 +++--
 variantapi/test/__init__.py    |   1 +
 variantapi/test/test_client.py |   1 +
 variantapi/test/variants.csv   |   0
 variantapi/test/variants.vcf   |  24 ++++++++
 9 files changed, 60 insertions(+), 162 deletions(-)
 delete mode 100755 annotate_vcf.py
 delete mode 100755 run.py
 create mode 100644 variantapi/test/__init__.py
 create mode 100644 variantapi/test/test_client.py
 create mode 100644 variantapi/test/variants.csv
 create mode 100644 variantapi/test/variants.vcf

diff --git a/MANIFEST.in b/MANIFEST.in
index fc709b3..9a07580 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,7 +1,8 @@
 include LICENSE
 include MANIFEST.in
-include README.rst
+include README.md
 include setup.py
-include run.py
+recursive-include variantapi/test *.csv
+recursive-include variantapi/test *.vcf
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
\ No newline at end of file
diff --git a/README.md b/README.md
index fb95b2e..2e1e483 100644
--- a/README.md
+++ b/README.md
@@ -4,22 +4,31 @@
 
 This client is still in beta but it is a good start to start playing around with the API.
 
+### Python versions
+Python version 3 is supported.
+
 ### Installation
+It is advised that you create a python virtual environment instead of globally installing the library
 
-Either download clone the repository from github and place the variantapi package
-within your code, or do
+There several ways to create a virtual environment but you can refer to [pip installation](https://pip.pypa.io/en/stable/installing/) and
+[virtualenv installation](https://virtualenv.pypa.io/en/stable/installation/) to first install these 2 tools if you don't
+have them already installed via a package manager (Linux) or HomeBrew (MacOS), etc.
 
-    pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
+To create a virtual env you can follow the [user guide](https://virtualenv.pypa.io/en/stable/userguide/) or simply run
+
+    virtualenv -p path_to/python3 venv_dir_name
+    
+Activate the virtual environment
 
-Installation on Linux:
-...
+    source venv_dir_name/bin/activate
 
-Installation on Mac OSX:
-- install pip using "sudo easy_install pip".
-- install the require Python libraries:  sudo pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
 
-Installation on Windows:
-...
+Finally to use the client either download or clone the repository from github and place the variantapi package
+within your code, or do
+
+    pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
+
+The client will be installed within your virtual environment.
 
 ### Test run
 
diff --git a/annotate_vcf.py b/annotate_vcf.py
deleted file mode 100755
index e0fe770..0000000
--- a/annotate_vcf.py
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import sys
-
-from variantapi.vcf import VCFAnnotator
-
-__author__ = 'ckopanos'
-
-
-def annotate_vcf(argv):
-    parser = argparse.ArgumentParser(description='VCF Annotator command line')
-    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True)
-    parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
-                        required=False, default='hg19')
-    parser.add_argument('-i',
-                        help='Path to vcf file',
-                        type=str, metavar='Input VCF File', required=True)
-    parser.add_argument('-o',
-                        help='Path to output vcf file',
-                        type=str, metavar='Output VCF File', required=False)
-    parser.add_argument('-p',
-                        help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
-                        type=str, metavar='Request Params', required=False, nargs='+')
-    parser.add_argument('-t', help='Run vcf annotator using x threads', type=int, default=3, required=False,
-                        metavar='Number of threads')
-    args = parser.parse_args()
-    api_key = args.k
-    vcf_file = args.i
-    output_vcf_file = args.o
-    ref_genome = args.g
-    num_threads = args.t
-    request_parameters = None
-    if args.p:
-        request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
-    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parameters=request_parameters,
-                                 max_threads=num_threads)
-    vcf_annotator.annotate(vcf_file, output_vcf_file)
-
-
-if __name__ == "__main__":
-    annotate_vcf(sys.argv[1:])
diff --git a/run.py b/run.py
deleted file mode 100755
index b4a8c1a..0000000
--- a/run.py
+++ /dev/null
@@ -1,105 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import json
-import sys
-import os
-
-from variantapi.client import VariantAPIClient
-
-__author__ = 'ckopanos'
-
-
-def annotate_variant(argv):
-    parser = argparse.ArgumentParser(description='Sample Variant API calls')
-    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
-    parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
-                        required=False, default='hg19')
-    parser.add_argument('-q',
-                        help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request '
-                             'e.g. chr19:20082943:1:G rs113488022. Don\'t use it together with the -i option',
-                        type=str, metavar='Query', required=False, nargs='+')
-    parser.add_argument('-p',
-                        help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
-                        type=str, metavar='Request Params', required=False, nargs='+')
-    parser.add_argument('-i',
-                        help='Path to text file with variants. It should include one variant per line. Don\'t use it '
-                             'together with the -q option',
-                        type=str, metavar='Text/CSV File one line per variant', required=False)
-    parser.add_argument('-o',
-                        help='Path to output file to store variant annotations',
-                        type=str, metavar='Output File with json entries', required=False)
-    args = parser.parse_args()
-    api_key = args.k
-    query = args.q
-    ref_genome = args.g
-    input_file = args.i
-    output_file = args.o
-    if query and input_file:
-        sys.stderr.write("Don't specify -i and -q options together. Use only one of them\n")
-        sys.exit(1)
-    if not query and not input_file:
-        sys.stderr.write("Please either specify -i or -q options\n")
-        sys.exit(1)
-    if input_file and not os.path.exists(input_file):
-        sys.stderr.write('File %s does not exist\n' % input_file)
-        sys.exit(1)
-    if output_file and os.path.exists(output_file):
-        sys.stderr.write('File %s already exists\n' % output_file)
-        sys.exit(1)
-    request_parameters = None
-    if args.p:
-        request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
-    api = VariantAPIClient(api_key)
-    if query:
-        if len(query) == 1:
-            result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome)
-        else:
-            if api_key is None:
-                sys.exit("You need to pass an api key to perform batch requests")
-            result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome)
-        sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
-        sys.stdout.write("\n")
-        sys.exit(0)
-    with open(input_file) as f:
-        variants = f.read().splitlines()
-    if variants:
-        if len(variants) > 1000:
-            sys.stdout.write('Too many variants.. Consider using annotate_vcf instead\n')
-            sys.stdout.flush()
-        write_f = None
-        if output_file:
-            write_f = open(output_file, 'w')
-        try:
-            if api_key is None:
-                results = []
-                for variant in variants:
-                    result = api.lookup(variant, params=request_parameters, ref_genome=ref_genome)
-                    if not result:
-                        result = {'error': 'Could not fetch annotations for %s' % variant}
-                    results.append(result)
-                if write_f is not None:
-                    json.dump(results, write_f, indent=4, sort_keys=True)
-                else:
-                    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
-                    sys.stdout.write("\n")
-            else:
-                result = api.batch_lookup(variants, params=request_parameters, ref_genome=ref_genome)
-                if write_f is not None:
-                    json.dump(result, write_f, indent=4, sort_keys=True)
-                else:
-                    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
-                    sys.stdout.write("\n")
-        except Exception as e:
-            # several things might occur. This is to broad, but lets not keep open file handles
-            sys.stderr.write(str(e))
-            sys.stderr.write("\n")
-            if write_f is not None:
-                write_f.close()
-            sys.exit(1)
-    else:
-        sys.stderr.write('No variants found in file %s\n' % input_file)
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    annotate_variant(sys.argv[1:])
diff --git a/setup.py b/setup.py
index a221c56..4b9ca81 100755
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,4 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 from os import path
 
 VERSION = (2, 0, '0b1')
@@ -10,16 +10,22 @@
 setup(
     name='variant_api',
     version=__versionstr__,
-    packages=['variantapi'],
+    packages=find_packages(".", ),
+    scripts=['scripts/variantapi_run.py', 'scripts/variantapi_annotate_vcf.py'],
     url='https://github.com/saphetor/variant-api-client-python',
     license='Apache License, Version 2.0',
-    package_data={'': ['annotate_vcf.py', 'run.py']},
-    author='Saphetor',
+    test_suite='variantapi.test.test_client.suite',
+    include_package_data=True,
+    package_data= {
+        '': ['*.vcf', '*.csv'],
+    },
+    author='Saphetor S.A.',
     author_email='support@saphetor.com',
     description='A basic python api client implementation for https://api.varsome.com',
     classifiers=[
         'Development Status :: 4 - Beta',
         'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
         'Operating System :: OS Independent',
         'License :: OSI Approved :: Apache License',
         'Programming Language :: Python :: 3',
@@ -28,10 +34,12 @@
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
     ],
     install_requires=[
         'requests>=2.0.0, <3.0.0',
         'PyVCF>=0.6.8',
         'jsonmodels>=2.2'
     ],
+    python_requires='>=3',
 )
diff --git a/variantapi/test/__init__.py b/variantapi/test/__init__.py
new file mode 100644
index 0000000..da44d8e
--- /dev/null
+++ b/variantapi/test/__init__.py
@@ -0,0 +1 @@
+__author__ = "ckopanos"
\ No newline at end of file
diff --git a/variantapi/test/test_client.py b/variantapi/test/test_client.py
new file mode 100644
index 0000000..da44d8e
--- /dev/null
+++ b/variantapi/test/test_client.py
@@ -0,0 +1 @@
+__author__ = "ckopanos"
\ No newline at end of file
diff --git a/variantapi/test/variants.csv b/variantapi/test/variants.csv
new file mode 100644
index 0000000..e69de29
diff --git a/variantapi/test/variants.vcf b/variantapi/test/variants.vcf
new file mode 100644
index 0000000..27d4500
--- /dev/null
+++ b/variantapi/test/variants.vcf
@@ -0,0 +1,24 @@
+##fileformat=VCFv4.1
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3

From 13e4b08fc9514fe105db045da1faa1f95f62b0c7 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Thu, 11 Jan 2018 10:35:50 +0200
Subject: [PATCH 07/31] Minor fixes in command line tools

---
 scripts/variantapi_run.py    | 13 +++++++---
 variantapi/client.py         |  2 +-
 variantapi/models/variant.py | 48 ++++++++++++++++++------------------
 variantapi/vcf.py            | 32 +++++++++++++++---------
 4 files changed, 56 insertions(+), 39 deletions(-)

diff --git a/scripts/variantapi_run.py b/scripts/variantapi_run.py
index b4a8c1a..a22e8b6 100755
--- a/scripts/variantapi_run.py
+++ b/scripts/variantapi_run.py
@@ -16,7 +16,7 @@ def annotate_variant(argv):
                         required=False, default='hg19')
     parser.add_argument('-q',
                         help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request '
-                             'e.g. chr19:20082943:1:G rs113488022. Don\'t use it together with the -i option',
+                             'e.g. chr15-73027478-T-C rs113488022. Don\'t use it together with the -i option',
                         type=str, metavar='Query', required=False, nargs='+')
     parser.add_argument('-p',
                         help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
@@ -57,8 +57,12 @@ def annotate_variant(argv):
             if api_key is None:
                 sys.exit("You need to pass an api key to perform batch requests")
             result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome)
-        sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
-        sys.stdout.write("\n")
+        if output_file:
+            write_f = open(output_file, 'w')
+            json.dump(result, write_f, indent=4, sort_keys=True)
+        else:
+            sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+            sys.stdout.write("\n")
         sys.exit(0)
     with open(input_file) as f:
         variants = f.read().splitlines()
@@ -71,6 +75,9 @@ def annotate_variant(argv):
             write_f = open(output_file, 'w')
         try:
             if api_key is None:
+                sys.stdout.write('Without an API key, variants will be annotated one a time, '
+                                 'causing a 429 too many requests error after some time\n')
+                sys.stdout.flush()
                 results = []
                 for variant in variants:
                     result = api.lookup(variant, params=request_parameters, ref_genome=ref_genome)
diff --git a/variantapi/client.py b/variantapi/client.py
index 46e9286..c680ee9 100755
--- a/variantapi/client.py
+++ b/variantapi/client.py
@@ -91,7 +91,7 @@ def get(self, path, params=None):
         response = self._make_request(path, "GET", params=params)
         return response.json()
 
-    def post(self, path, params=None, json_data=None, raise_exceptions=False):
+    def post(self, path, params=None, json_data=None, raise_exceptions=True):
         # handle api errors in batch requests.
         try:
             response = self._make_request(path, "POST", params=params, json_data=json_data)
diff --git a/variantapi/models/variant.py b/variantapi/models/variant.py
index e200554..22d9cc2 100755
--- a/variantapi/models/variant.py
+++ b/variantapi/models/variant.py
@@ -3,6 +3,7 @@
 
 __author__ = "ckopanos"
 
+
 class AnnotatedVariant(models.Base):
     """
     Base variant result definition model
@@ -15,33 +16,34 @@ class AnnotatedVariant(models.Base):
     ref = fields.StringField(help_text="REF Sequence", required=False, nullable=True)
     pos = fields.IntField(help_text="Position")
     variant_id = fields.StringField(help_text='Variant Id')
-    refseq_transcripts = fields.ListField(required=False, items_types=(Transcript, ), help_text="RefSeq Transcripts")
+    refseq_transcripts = fields.ListField(required=False, items_types=(Transcript,), help_text="RefSeq Transcripts")
     ensembl_transcripts = fields.ListField(required=False, items_types=(Transcript,), help_text="Ensembl Transcripts")
     broad_exac = fields.ListField(required=False, items_types=(ExAC,), help_text="ExAC")
-    gnomad_exomes = fields.ListField(required=False, items_types=(GnomAD, ), help_text="gnomAD Exomes (ExAC)")
-    gnomad_exomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage, ), help_text="gnomAD exomes coverage")
+    gnomad_exomes = fields.ListField(required=False, items_types=(GnomAD,), help_text="gnomAD Exomes (ExAC)")
+    gnomad_exomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage,),
+                                              help_text="gnomAD exomes coverage")
     gnomad_genomes = fields.ListField(required=False, items_types=(GnomAD,), help_text="gnomAD Genomes")
-    gnomad_genomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage,), help_text="gnomAD genomes coverage")
-    thousand_genomes = fields.ListField(required=False, items_types=(ThousandGenomes, ), help_text="1000 Genomes")
+    gnomad_genomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage,),
+                                               help_text="gnomAD genomes coverage")
+    thousand_genomes = fields.ListField(required=False, items_types=(ThousandGenomes,), help_text="1000 Genomes")
     gerp = fields.ListField(required=False, items_types=(Gerp,), help_text="GERP")
-    isb_kaviar3 = fields.ListField(required=False, items_types=(Kaviar3, ), help_text='ISB Kaviar3')
-    dbnsfp = fields.ListField(required=False, items_types=(DbNSFP, ), help_text="dbNSFP")
-    dann_snvs = fields.ListField(required=False, items_types=(DannSNVs, ), help_text="DANN score")
-    dbnsfp_dbscsnv = fields.ListField(required=False, items_types=(DBscSNV, ), help_text='dbNSFP dbscSNV')
-    ncbi_dbsnp = fields.ListField(required=False, items_types=(DbSNP, ), help_text="dbSNP")
-    sanger_cosmic = fields.ListField(required=False, items_types=(Cosmic, ), help_text="Sanger Cosmic")
-    sanger_cosmic_public = fields.ListField(required=False, items_types=(CosmicPublic, ), help_text="Cosmic")
-    sanger_cosmic_licensed = fields.ListField(required=False, items_types=(CosmicLicensed, ), help_text="Cosmic")
-    ncbi_clinvar = fields.ListField(required=False, items_types=(ClinVar, ), help_text="ClinVar")
-    ncbi_clinvar2 = fields.ListField(required=False, items_types=(ClinVar2, ), help_text="ClinVar2")
-    icgc_somatic = fields.ListField(required=False, items_types=(Somatic, ), help_text="ICGC Somatic")
-    iarc_tp53_germline = fields.ListField(required=False, items_types=(TP53Germline, ), help_text="IARC TP53 Germline")
-    iarc_tp53_somatic = fields.ListField(required=False, items_types=(TP53Somatic, ), help_text="IARC TP53 Somatic")
+    isb_kaviar3 = fields.ListField(required=False, items_types=(Kaviar3,), help_text='ISB Kaviar3')
+    dbnsfp = fields.ListField(required=False, items_types=(DbNSFP,), help_text="dbNSFP")
+    dann_snvs = fields.ListField(required=False, items_types=(DannSNVs,), help_text="DANN score")
+    dbnsfp_dbscsnv = fields.ListField(required=False, items_types=(DBscSNV,), help_text='dbNSFP dbscSNV')
+    ncbi_dbsnp = fields.ListField(required=False, items_types=(DbSNP,), help_text="dbSNP")
+    sanger_cosmic = fields.ListField(required=False, items_types=(Cosmic,), help_text="Sanger Cosmic")
+    sanger_cosmic_public = fields.ListField(required=False, items_types=(CosmicPublic,), help_text="Cosmic")
+    sanger_cosmic_licensed = fields.ListField(required=False, items_types=(CosmicLicensed,), help_text="Cosmic")
+    ncbi_clinvar = fields.ListField(required=False, items_types=(ClinVar,), help_text="ClinVar")
+    ncbi_clinvar2 = fields.ListField(required=False, items_types=(ClinVar2,), help_text="ClinVar2")
+    icgc_somatic = fields.ListField(required=False, items_types=(Somatic,), help_text="ICGC Somatic")
+    iarc_tp53_germline = fields.ListField(required=False, items_types=(TP53Germline,), help_text="IARC TP53 Germline")
+    iarc_tp53_somatic = fields.ListField(required=False, items_types=(TP53Somatic,), help_text="IARC TP53 Somatic")
     pub_med_articles = DictField(required=False, help_text="PUBMED Articles")
-    uniprot_variants = fields.ListField(required=False, items_types=(UniprotVariants, ), help_text="UniProt variants")
-    wustl_civic = fields.ListField(required=False, items_types=(Civic, ), help_text="CIViC")
-    gwas = fields.ListField(required=False, items_types=(GWAS, ), help_text="GWAS")
-
+    uniprot_variants = fields.ListField(required=False, items_types=(UniprotVariants,), help_text="UniProt variants")
+    wustl_civic = fields.ListField(required=False, items_types=(Civic,), help_text="CIViC")
+    gwas = fields.ListField(required=False, items_types=(GWAS,), help_text="GWAS")
 
     @property
     def genes(self):
@@ -84,5 +86,3 @@ def gnomad_exomes_af(self):
     def gnomad_genomes_af(self):
         af = [gnomad_genomes.af for gnomad_genomes in self.gnomad_genomes]
         return af[0] if af else None
-
-
diff --git a/variantapi/vcf.py b/variantapi/vcf.py
index 4352c0a..052ae06 100755
--- a/variantapi/vcf.py
+++ b/variantapi/vcf.py
@@ -68,36 +68,46 @@ def annotate_record(self, record, variant_result):
         record.INFO['variant_id'] = variant_result.variant_id
         record.INFO['gene'] = ",".join(variant_result.genes)
         record.INFO['gnomad_exomes_AF'] = variant_result.gnomad_exomes_af
-        record.INFO['gnomad_genomes_AF'] = variant_result.gnomad_exomes_af
+        record.INFO['gnomad_genomes_AF'] = variant_result.gnomad_genomes_af
         record.ALT = variant_result.alt
         record.POS = variant_result.pos
         record.ID = ";".join(variant_result.rs_ids) or "."
         return record
 
-    def add_vcf_header_info(self, vcf_writer):
+    def add_vcf_header_info(self, vcf_template):
         """
         Adds vcf INFO headers for the annotated values provided
         This is just a base method you need to override in your own implementation
         depending on the annotations added through the annotate_record method
-        :param vcf_writer: vcf writer object
+        :param vcf_template: vcf reader object
         :return:
         """
-        vcf_writer.infos['variant_id'] = _Info('variant_id', 1, 'Integer', 'Saphetor variant identifier', None, None)
-        vcf_writer.infos['gene'] = _Info('gene', '.', 'String', 'Genes related to this variant', None, None)
-        vcf_writer.infos['gnomad_exomes_AF'] = _Info('gnomad_exomes_AF', '.', 'Float',
+        vcf_template.infos['variant_id'] = _Info('variant_id', 1, 'Integer', 'Saphetor variant identifier', None, None)
+        vcf_template.infos['gene'] = _Info('gene', '.', 'String', 'Genes related to this variant', None, None)
+        vcf_template.infos['gnomad_exomes_AF'] = _Info('gnomad_exomes_AF', '.', 'Float',
                                                      'GnomAD exomes allele frequency value', None, None)
-        vcf_writer.infos['gnomad_genomes_AF'] = _Info('gnomad_genomes_AF', '.', 'Float',
+        vcf_template.infos['gnomad_genomes_AF'] = _Info('gnomad_genomes_AF', '.', 'Float',
                                                       'GnomAD genomes allele frequency value', None, None)
 
-    def annotate(self, input_vcf_file, output_vcf_file=None):
+    def annotate(self, input_vcf_file, output_vcf_file=None, template=None, **kwargs):
+        """
+        :param input_vcf_file: The input vcf file to be annotated
+        :param output_vcf_file: The file to write annotations back if none input_vcf_file.annotated.vcf will be
+        generated instead
+        :param template: An alternate vcf file to use for vcf file headers. If none the input vcf file will
+        be used
+        :return:
+        """
         annotations_start = time.time()
         if not os.path.isfile(input_vcf_file):
             raise FileNotFoundError('%s does not exist' % input_vcf_file)
         if output_vcf_file is None:
             output_vcf_file = "%s.annotated.vcf" % input_vcf_file
-        vcf_reader = vcf.Reader(filename=input_vcf_file, strict_whitespace=True)
-        self.vcf_writer = vcf.Writer(open(output_vcf_file, 'w'), vcf_reader)
-        self.add_vcf_header_info(self.vcf_writer)
+        vcf_reader = vcf.Reader(filename=input_vcf_file, strict_whitespace=kwargs.get('strict_whitespace', True))
+        vcf_template = vcf_reader if template is None else vcf.Reader(filename=template, strict_whitespace=kwargs.get(
+            'strict_whitespace', True))
+        self.add_vcf_header_info(vcf_template)
+        self.vcf_writer = vcf.Writer(open(output_vcf_file, 'w'), vcf_template)
         input_batch = OrderedDict()
         # this will keep the request queue large enough so that parallel requests will not stop executing
         batch_limit = self.max_variants_per_batch * self.max_threads * 2

From 4a4f4f77610807c6d24830a0777d91f944ccbc84 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Thu, 11 Jan 2018 17:20:58 +0200
Subject: [PATCH 08/31] Updated documentation

---
 README.md                    | 145 +++++++++++++++++++++++++++--------
 variantapi/models/variant.py |  39 +++++++++-
 2 files changed, 153 insertions(+), 31 deletions(-)

diff --git a/README.md b/README.md
index 2e1e483..7f847c7 100644
--- a/README.md
+++ b/README.md
@@ -28,30 +28,35 @@ within your code, or do
 
     pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
 
-The client will be installed within your virtual environment.
+The client will be installed within your virtual environment. Also 2 scripts called variantapi_run.py and 
+variantapi_annotate_vcf.py will be available within your virtual environment $PATH
 
-### Test run
+### Using the scripts to directly annotate a list of variants or a vcf file
 
+#### Annotating a variant or list of variants
 Try the following query to annotate a single variant:
-./run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
 
-The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensemble_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
-
-You are now ready to write your own code using the VarSome API.
-
-### API Documentation
-
-Please visit the [api documentation](http://docs.varsome.apiary.io) to find out how to use the api and
-what values does the api provide as a response to lookup requests
+    variantapi_run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
 
-### How to get an API key
+The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensemble_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
+The script may also accept a txt file with variants (one per line) and an optional output file to store the
+annotations to. It is advised that you don't use this script with a large number of variants but directly use
+the client within your code.
 
-You generally are not required to have an api key to use the api, though the number of requests you will be able
-to issue will be throttled if they exceed a certain number.
+    variantapi_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1
+    
+Will read variants from variants.txt and dump the annotations to annotations.txt. If you don't use the -k
+parameter the script will do as many requests as the variants within variants.txt file and you will probably
+end up with HTTP status code 429 (Too many requests) error.
 
-An API key is required in order to batch requests or enable allele frequency filtering.
+#### Annotating a vcf file
+To annotate a vcf file use:
 
-To obtain an API key please [contact us](mailto:support@saphetor.com)
+    variantapi_annotate_vcf.py -g hg19 -k api_key -i input.vcf -o annotated_vcf.vcf -p add-all-data=1
+    
+Notice however that not all available annotations will be present in the annotated_vcf file. Only a subset
+of the returned annotations will be available, when running this script. Have a look at "Using the client in your code" 
+section on how to annotate a vcf file with the annotations that are of interest to you. 
 
 ### Using the client in your code
 
@@ -65,13 +70,14 @@ your code use
     # if you don't have an api key use
     # api = VariantAPIClient()
     # fetch information about a variant into a dictionary
-    result = api.lookup('chr19:20082943:1:G', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
+    result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
     # access results e.g. the transcripts of the variant
     transcripts = result['refseq_transcripts']
     # fetch information for multiple variants
     variants = ['chr19:20082943:1:G','chr22:39777823::CAA']
     # results will be an array of dictionaries an api key will be required for this request
     results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19')
+    # look at the python doc for batch_lookup method for additional parameters
 
 If errors occur while using the client an exception will be thrown.
 You may wish to catch this exception and proceed with your own code logic
@@ -84,27 +90,106 @@ You may wish to catch this exception and proceed with your own code logic
         # proceed with your code flow e.g.
         print(e) # 404 (invalid reference genome)
 
-### Example Usage
+To view available request parameters (used in the params method parameter) refer to an example at [api.varsome.com](https://api.varsome.com)
 
+To understand how annotation properties are included in the json response please refer to the relevant [schema](https://api.varsome.com/lookup/schema)
 
-You may download and run the run.py python file after installation of the package
-to test the api client directly e.g.
+#### JSON response wrapper
 
-    ./run.py -g hg19 -q 'chr19:20082943:1:G' -p add-all-data=1
+If you don't want to read through each attribute in the json response you can wrap the result into a Python
+[json model](http://jsonmodels.readthedocs.io/en/latest/readme.html).
 
-You may pass more than one values after the -q argument that will make a batch request
-to the API but you will need a token to do that e.g.
+    from variantapi.client import VariantAPIClient
+    from variantapi.models.variant import AnnotatedVariant
+    # api key is not required for single variant lookups
+    api_key = 'Your token'
+    api = VariantAPIClient(api_key)
+    # fetch information about a variant into a dictionary
+    result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
+    annotated_variant = AnnotatedVariant(**result)
 
-    ./run.py -k 'your token' -g hg19 -q 'rs113488022' 'chr19:20082943:1:G' -p add-source-databases=gnomad-exomes,gnomad-genomes
+now you have access to a set of shortcut attributes (these will be updated over time in the code base)
 
-Run
+    annotated_variant.chromosome
+    annotated_variant.alt
+    annotated_variant.genes # directly get the genes related to the variant
+    annotated_variant.gnomad_exomes_af # etc
 
-    ./run.py -h
+or you may access other inner properties of other available properties
 
-for a list of available options
+    # get gnomad exomes allele number
+    allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes]
 
-To view available request parameters (used in the params method parameter) refer to an example at [api.varsome.com](https://api.varsome.com) or
-the [api documentation](http://docs.varsome.apiary.io).
+annotated_variant.gnomad_exomes and also other json model type of objects that contain a version property, are
+always returned as lists of objects. This is because of the ability of the API to return multiple versions of 
+annotation databases (though this is not currently publicly available). For consistency reasons therefore
+these are always lists, though it is safe to assume that they will only include a single item. So it is safe
+to rewrite as:
+     
+    try:
+        allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes][0]
+    except IndexError:
+        pass # no gnomad exomes annotation for the variant
+           
+#### Annotating a VCF using the client
+
+To annotate a vcf you can base your code on the VCFAnnotator object. This provides a basic implementation that
+will annotate a vcf file using a set of the available annotations. It uses [PyVCF](https://github.com/jamescasbon/PyVCF) to read and write to vcf files.
+
+    from variantapi.vcf import VCFAnnotator
+    api_key = 'Your token'
+    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
+    vcf_file = 'input.vcf'
+    output_vcf_file = 'annotated.vcf'
+    vcf_annotator.annotate(vcf_file, output_vcf_file)
+        
+To annotate the vcf file with the annotations that you are interested in you need only override 2 methods
+in the VCFAnnotator class
+
+    from variantapi.vcf import VCFAnnotator
+    from vcf.parser import _Info
+    class MyVCFAnnotator(VCFAnnotator):
+    
+        def annotate_record(self, record, variant_result):
+            """
+            :param record: vcf record object
+            :param variant_result: AnnotatedVariant object
+            :return: annotated record object
+            """
+            record.INFO['gnomad_exomes_AN'] = variant_result.gnomad_exomes_an
+            return record
+        
+            
+        def add_vcf_header_info(self, vcf_template):
+            """
+            Adds vcf INFO headers for the annotated values provided
+            This is just a base method you need to override in your own implementation
+            depending on the annotations added through the annotate_record method
+            :param vcf_template: vcf reader object
+            :return:
+            """
+            vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer',
+                                                                 'GnomAD exomes allele number value', None, None)
+                                                                 
+    api_key = 'Your token'
+    vcf_annotator = MyVCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
+    vcf_file = 'input.vcf'
+    output_vcf_file = 'annotated.vcf'
+    vcf_annotator.annotate(vcf_file, output_vcf_file)
+        
+        
+### API Documentation
+
+Please visit the [api documentation](https://api.varsome.com) to find out how to use the api and
+what values does the api provide as a response to lookup requests
+
+### How to get an API key
+
+You generally are not required to have an api key to use the api, though the number of requests you will be able
+to issue will be throttled if they exceed a certain number.
+
+An API key is required in order to batch requests or enable allele frequency filtering.
+
+To obtain an API key please [contact us](mailto:support@saphetor.com)
 
-To understand how annotation properties are included in the json response please refer to the relevant [schema](https://api.varsome.com/lookup/schema)
 
diff --git a/variantapi/models/variant.py b/variantapi/models/variant.py
index 22d9cc2..563eb08 100755
--- a/variantapi/models/variant.py
+++ b/variantapi/models/variant.py
@@ -47,6 +47,10 @@ class AnnotatedVariant(models.Base):
 
     @property
     def genes(self):
+        """
+
+        :return: list of genes
+        """
         genes = []
         genes.extend(self.refseq_genes)
         genes.extend(self.ensembl_genes)
@@ -54,6 +58,10 @@ def genes(self):
 
     @property
     def refseq_genes(self):
+        """
+
+        :return: list of genes found in RefSeq transcripts
+        """
         genes = []
         for transcript in self.refseq_transcripts:
             genes.extend([item.gene_symbol for item in transcript.items if item.gene_symbol])
@@ -61,6 +69,10 @@ def refseq_genes(self):
 
     @property
     def ensembl_genes(self):
+        """
+
+        :return: list of genes found in Ensembl transcripts
+        """
         genes = []
         for transcript in self.ensembl_transcripts:
             genes.extend([item.gene_symbol for item in transcript.items if item.gene_symbol])
@@ -68,6 +80,10 @@ def ensembl_genes(self):
 
     @property
     def rs_ids(self):
+        """
+
+        :return: list of rsids (str)
+        """
         rs_ids = []
         for dbnsp_entry in self.ncbi_dbsnp:
             rs_ids.extend(dbnsp_entry.rsid)
@@ -77,12 +93,33 @@ def rs_ids(self):
     def gnomad_exomes_af(self):
         """
         Returns the gnomad exomes af value.
-        :return:
+        :return: float gnomad exomes af
         """
         af = [gnomad_exomes.af for gnomad_exomes in self.gnomad_exomes]
         return af[0] if af else None
 
     @property
     def gnomad_genomes_af(self):
+        """
+        Returns the gnomad genomes af value.
+        :return: float gnomad genomes af
+        """
         af = [gnomad_genomes.af for gnomad_genomes in self.gnomad_genomes]
         return af[0] if af else None
+
+    @property
+    def gnomad_exomes_an(self):
+        """
+
+        :return: int gnomad exomes an
+        """
+        an = [gnomad_exomes.an for gnomad_exomes in self.gnomad_exomes]
+        return an[0] if an else None
+
+    @property
+    def gnomad_genomes_an(self):
+        """
+        :return: int gnomad genomes an
+        """
+        an = [gnomad_genomes.an for gnomad_genomes in self.gnomad_genomes]
+        return an[0] if an else None

From 6cfb6d846c96d2ceefcdccf9c356cb449143e58b Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Thu, 11 Jan 2018 17:56:46 +0200
Subject: [PATCH 09/31] Updated documentation

---
 README.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/README.md b/README.md
index 7f847c7..2a45874 100644
--- a/README.md
+++ b/README.md
@@ -163,8 +163,6 @@ in the VCFAnnotator class
         def add_vcf_header_info(self, vcf_template):
             """
             Adds vcf INFO headers for the annotated values provided
-            This is just a base method you need to override in your own implementation
-            depending on the annotations added through the annotate_record method
             :param vcf_template: vcf reader object
             :return:
             """

From 9bb0c88c37f8e2fd8cbda3b28c5576c522a93caa Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 11:01:48 +0200
Subject: [PATCH 10/31] Added unit tests

---
 setup.py                               |    3 +-
 variantapi/test/test_client.py         |    1 -
 variantapi/test/variants.csv           |    0
 variantapi/test/variants.vcf           |   24 -
 variantapi/{test => tests}/__init__.py |    0
 variantapi/tests/test_client.py        |  128 +
 variantapi/tests/variants.csv          | 3000 ++++++++++++++++++++++++
 variantapi/tests/variants.vcf          |  156 ++
 8 files changed, 3286 insertions(+), 26 deletions(-)
 delete mode 100644 variantapi/test/test_client.py
 delete mode 100644 variantapi/test/variants.csv
 delete mode 100644 variantapi/test/variants.vcf
 rename variantapi/{test => tests}/__init__.py (100%)
 create mode 100644 variantapi/tests/test_client.py
 create mode 100644 variantapi/tests/variants.csv
 create mode 100644 variantapi/tests/variants.vcf

diff --git a/setup.py b/setup.py
index 4b9ca81..a0af3d0 100755
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,8 @@
     scripts=['scripts/variantapi_run.py', 'scripts/variantapi_annotate_vcf.py'],
     url='https://github.com/saphetor/variant-api-client-python',
     license='Apache License, Version 2.0',
-    test_suite='variantapi.test.test_client.suite',
+    test_suite='nose.collector',
+    tests_require=['nose'],
     include_package_data=True,
     package_data= {
         '': ['*.vcf', '*.csv'],
diff --git a/variantapi/test/test_client.py b/variantapi/test/test_client.py
deleted file mode 100644
index da44d8e..0000000
--- a/variantapi/test/test_client.py
+++ /dev/null
@@ -1 +0,0 @@
-__author__ = "ckopanos"
\ No newline at end of file
diff --git a/variantapi/test/variants.csv b/variantapi/test/variants.csv
deleted file mode 100644
index e69de29..0000000
diff --git a/variantapi/test/variants.vcf b/variantapi/test/variants.vcf
deleted file mode 100644
index 27d4500..0000000
--- a/variantapi/test/variants.vcf
+++ /dev/null
@@ -1,24 +0,0 @@
-##fileformat=VCFv4.1
-##fileDate=20090805
-##source=myImputationProgramV3.1
-##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
-##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
-##phasing=partial
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
-##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
-##FILTER=<ID=q10,Description="Quality below 10">
-##FILTER=<ID=s50,Description="Less than 50% of samples have data">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
-20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
-20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
-20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
-20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/variantapi/test/__init__.py b/variantapi/tests/__init__.py
similarity index 100%
rename from variantapi/test/__init__.py
rename to variantapi/tests/__init__.py
diff --git a/variantapi/tests/test_client.py b/variantapi/tests/test_client.py
new file mode 100644
index 0000000..c968919
--- /dev/null
+++ b/variantapi/tests/test_client.py
@@ -0,0 +1,128 @@
+import os
+import unittest
+from tempfile import NamedTemporaryFile
+
+import vcf
+from vcf.parser import _Info
+from variantapi.client import VariantAPIClient, VariantApiException
+from variantapi.models.variant import AnnotatedVariant
+from variantapi.vcf import VCFAnnotator
+
+__author__ = "ckopanos"
+
+API_KEY = os.getenv('VARIANT_API_KEY', None)
+BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+VARIANTS_CSV_FILE = os.path.join(BASE_DIR, 'tests', 'variants.csv')
+VARIANTS_VCF_FILE = os.path.join(BASE_DIR, 'tests', 'variants.vcf')
+
+
+class TestApiClient(unittest.TestCase):
+
+    def __init__(self, methodName='runTest'):
+        super().__init__(methodName)
+        self.client = VariantAPIClient(API_KEY)
+        with open(VARIANTS_CSV_FILE) as f:
+            self.variants_to_lookup = f.read().splitlines()
+        if API_KEY is None:
+            # just get 5 variants without an API key tests might fail with 429
+            self.variants_to_lookup = self.variants_to_lookup[:5]
+        else:
+            self.variants_to_lookup = self.variants_to_lookup[:50]
+
+    def tearDown(self):
+        self.client.session.close()
+
+    def test_schema(self):
+        """Check we receive the response schema back"""
+        self.assertIsNotNone(self.client.schema())
+
+    def test_404(self):
+        """Check we can raise VariantApiException"""
+        with self.assertRaises(VariantApiException) as ve:
+            self.client.lookup('chrM:410:A:T', ref_genome='hg64')
+        test_exception = ve.exception
+        self.assertEqual(test_exception.status, 404)
+
+    def test_get_lookup_hg19(self):
+        """Check we can do plain get requests"""
+        for i, variant in enumerate(self.variants_to_lookup):
+            with self.subTest(i=i):
+                result = self.client.lookup(variant, ref_genome='hg19', params={'add-all-data': 1,
+                                                                                'expand-pubmed-articles': 0})
+                self.assertIsNotNone(result)
+                self.assertTrue('variant_id' in result)
+
+    def test_batch_lookup_hg19(self):
+        """Check we can do batch requests"""
+        results = self.client.batch_lookup(self.variants_to_lookup, ref_genome='hg19',
+                                           params={'add-all-data': 1, 'expand-pubmed-articles': 0},
+                                           raise_exceptions=True)
+        self.assertEqual(len(results), len(self.variants_to_lookup))
+
+
+class TestApiResponse(unittest.TestCase):
+
+    def __init__(self, methodName='runTest'):
+        super().__init__(methodName)
+        client = VariantAPIClient(API_KEY, max_variants_per_batch=1000)
+        with open(VARIANTS_CSV_FILE) as f:
+            self.variants_to_lookup = f.read().splitlines()
+        self.results = client.batch_lookup(self.variants_to_lookup, ref_genome='hg19',
+                                           params={'add-all-data': 1, 'expand-pubmed-articles': 0},
+                                           raise_exceptions=True)
+
+    def test_result_is_not_none(self):
+        """Check result is not None"""
+        for i, result in enumerate(self.results):
+            with self.subTest(i=i):
+                self.assertIsNotNone(result)
+
+    def test_result_has_variant_id(self):
+        """Check result includes variant_id"""
+        for i, result in enumerate(self.results):
+            with self.subTest(i=i):
+                self.assertTrue('variant_id' in result)
+
+    def test_variant_chromosome_result_chromosome(self):
+        """Check that the requested chromosome is the same as the one returned"""
+        for i, result in enumerate(self.results):
+            with self.subTest(i=i):
+                chromosome = self.variants_to_lookup[i].split(":")[0]
+                self.assertEqual(result['chromosome'], chromosome)
+
+    def test_result_wrapper(self):
+        """Check that we can wrap the result in a json model"""
+        for i, result in enumerate(self.results):
+            with self.subTest(i=i):
+                annotated_variant = AnnotatedVariant(**result)
+                self.assertEqual(annotated_variant.chromosome, result['chromosome'])
+                self.assertIsNotNone(annotated_variant.pos)
+                self.assertEqual(result['pos'], annotated_variant.pos)
+
+
+class TestVCFAnnotator(VCFAnnotator):
+
+    def annotate_record(self, record, variant_result):
+        record.INFO['gnomad_genomes_AN'] = variant_result.gnomad_genomes_an
+        return record
+
+    def add_vcf_header_info(self, vcf_template):
+        vcf_template.infos['gnomad_genomes_AN'] = _Info('gnomad_genomes_AN', '.', 'Integer',
+                                                        'GnomAD genomes allele number value', None, None)
+
+class TestVcfAnnotator(unittest.TestCase):
+
+    def __init__(self, methodName='runTest'):
+        super().__init__(methodName)
+        self.annotator = TestVCFAnnotator(API_KEY)
+
+    def test_annotate_vcf(self):
+        """Check that we can annotate a vcf file"""
+        output_vcf_file = NamedTemporaryFile(delete=False)
+        self.annotator.annotate(VARIANTS_VCF_FILE, output_vcf_file.name)
+        vcf_reader = vcf.Reader(filename=output_vcf_file.name, strict_whitespace=True)
+        self.assertTrue('gnomad_genomes_AN' in vcf_reader.infos)
+        for i, record in enumerate(vcf_reader):
+            with self.subTest(i=i):
+                self.assertTrue('gnomad_genomes_AN' in record.INFO)
+
diff --git a/variantapi/tests/variants.csv b/variantapi/tests/variants.csv
new file mode 100644
index 0000000..22266e1
--- /dev/null
+++ b/variantapi/tests/variants.csv
@@ -0,0 +1,3000 @@
+chr18:31400047:A:G
+chr9:33797928:G:GCC
+chr9:108419525:T:A
+chr8:42798225:T:G
+chr5:158703735:T:C
+chr12:125451487:C:T
+chrX:53055916:A:G
+chr10:15505648:C:A
+chr1:81398346:A:C
+chr11:34134595:A:T
+chr1:202573181:C:A
+chr14:36622555:G:A
+chr2:115578379:C:T
+chr17:44317259:C:A
+chr1:179630010:G:A
+chrX:19380975:TA:T
+chr2:59847178:C:T
+chr1:200182664:C:T
+chr4:37823502:TAAAAAAAAAA:T
+chr14:41832822:C:A
+chr20:2198507:G:T
+chr3:41599916:C:A
+chr2:154953165:A:G
+chr4:66717200:A:G
+chr4:176209042:G:T
+chr4:111381638:C:T
+chr7:150234408:G:C
+chr9:100227011:T:C
+chr18:34789800:A:G
+chr17:21551377:G:A
+chr8:99141814:T:C
+chr2:62067880:G:C
+chr4:167250749:T:A
+chr2:91885946:T:C
+chr17:16847907:G:A
+chr21:25819367:C:T
+chr14:100157791:T:A
+chr2:234359375:A:G
+chr7:73666736:CA:C
+chr2:3773488:C:T
+chr11:2187477:C:T
+chr1:970550:GG:G
+chr6:32486711:A:T
+chr4:95500499:A:G
+chr22:50318665:G:C
+chr7:47977325:T:C
+chr5:131676688:T:G
+chr1:59794538:C:T
+chr1:237819014:C:G
+chr22:39283187:A:C
+chr10:27277408:G:A
+chr4:190596205:T:C
+chr1:237435522:C:A
+chr11:121341150:C:T
+chr1:196757258:C:T
+chr17:40049694:G:A
+chr3:154204766:G:A
+chr6:155472090:G:A
+chr1:202842935:C:T
+chr2:15537641:T:C
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\ No newline at end of file
diff --git a/variantapi/tests/variants.vcf b/variantapi/tests/variants.vcf
new file mode 100644
index 0000000..906a5b4
--- /dev/null
+++ b/variantapi/tests/variants.vcf
@@ -0,0 +1,156 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[reads.bam] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=[chr22:42020321-42527953] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=CALCULATE_AS_NECESSARY baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=2 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=gatk.log help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.15 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name=dbsnp source=/data/reference/dbSNP_132/dbsnp_132.hg19.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr10,length=135534747,assembly=hg19>
+##contig=<ID=chr11,length=135006516,assembly=hg19>
+##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
+##contig=<ID=chr12,length=133851895,assembly=hg19>
+##contig=<ID=chr13,length=115169878,assembly=hg19>
+##contig=<ID=chr14,length=107349540,assembly=hg19>
+##contig=<ID=chr15,length=102531392,assembly=hg19>
+##contig=<ID=chr16,length=90354753,assembly=hg19>
+##contig=<ID=chr17,length=81195210,assembly=hg19>
+##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
+##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
+##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
+##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
+##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
+##contig=<ID=chr18,length=78077248,assembly=hg19>
+##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
+##contig=<ID=chr19,length=59128983,assembly=hg19>
+##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
+##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
+##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
+##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr20,length=63025520,assembly=hg19>
+##contig=<ID=chr21,length=48129895,assembly=hg19>
+##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
+##contig=<ID=chr22,length=51304566,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
+##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
+##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
+##contig=<ID=chr5,length=180915260,assembly=hg19>
+##contig=<ID=chr6,length=171115067,assembly=hg19>
+##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
+##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
+##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
+##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
+##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
+##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
+##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
+##contig=<ID=chr7,length=159138663,assembly=hg19>
+##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
+##contig=<ID=chr8,length=146364022,assembly=hg19>
+##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
+##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
+##contig=<ID=chr9,length=141213431,assembly=hg19>
+##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
+##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
+##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
+##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
+##contig=<ID=chrM,length=16571,assembly=hg19>
+##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
+##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
+##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
+##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
+##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
+##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
+##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
+##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
+##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
+##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
+##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
+##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
+##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
+##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
+##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
+##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
+##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
+##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
+##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
+##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
+##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
+##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
+##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
+##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
+##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
+##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
+##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
+##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
+##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
+##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
+##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
+##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
+##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
+##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
+##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
+##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
+##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
+##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
+##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
+##contig=<ID=chrX,length=155270560,assembly=hg19>
+##contig=<ID=chrY,length=59373566,assembly=hg19>
+##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BLANK	NA12878	NA12891	NA12892	NA19238	NA19239	NA19240
+chr22	42522392	rs28371738	G	A	2951.95	.	AC=2;AF=0.143;AN=14;BaseQRankSum=0.375;DB;DP=1506;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=123.5516;MQ=253.92;MQ0=0;MQRankSum=0.685;QD=5.90;ReadPosRankSum=0.590	GT:AD:DP:GQ:PL	0/0:6,0:6:18.04:0,18,211	0/1:138,107:250:99:1961,0,3049	0/1:169,77:250:99:1038,0,3533	0/0:249,0:250:99:0,600,5732	0/0:248,1:250:99:0,627,6191	0/0:250,0:250:99:0,615,5899	0/0:250,0:250:99:0,579,5674
+chr22	42522613	rs1135840	G	C	11611.03	.	AC=6;AF=0.429;AN=14;BaseQRankSum=16.289;DB;DP=1518;DS;Dels=0.03;FS=0.000;HRun=0;HaplotypeScore=142.5716;MQ=242.46;MQ0=0;MQRankSum=2.010;QD=9.16;ReadPosRankSum=-1.731	GT:AD:DP:GQ:PL	0/1:13,4:17:62.64:63,0,296	0/1:118,127:246:99:2396,0,1719	0/0:241,0:244:99:0,459,4476	0/1:161,85:246:99:1489,0,2353	0/1:110,132:242:99:2561,0,1488	0/1:106,135:242:99:2613,0,1389	0/1:116,126:243:99:2489,0,1537
+chr22	42522755	.	C	G	36.98	.	AC=1;AF=0.071;AN=14;BaseQRankSum=-14.866;DP=1527;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=253.4254;MQ=197.36;MQ0=2;MQRankSum=-10.810;QD=0.15;ReadPosRankSum=-17.244	GT:AD:DP:GQ:PL	0/0:26,1:27:51.08:0,51,570	0/0:208,40:248:99:0,236,4169	0/0:192,56:249:99:0,114,4292	0/1:179,66:245:75.42:75,0,3683	0/0:214,32:246:99:0,172,4235	0/0:200,49:249:61.05:0,61,4049	0/0:195,50:246:32.07:0,32,3757
+chr22	42523003	rs116917064	A	G	7113.55	.	AC=8;AF=0.571;AN=14;BaseQRankSum=6.026;DB;DP=1433;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=101.7894;MQ=182.04;MQ0=0;MQRankSum=-2.501;QD=4.96;ReadPosRankSum=8.294	GT:AD:DP:GQ:PL	0/1:10,2:12:0.62:1,0,257	1/1:9,173:183:99:2385,273,0	0/1:153,95:249:99:355,0,2355	0/1:140,110:250:99:1334,0,2242	0/1:164,85:249:99:1070,0,2279	0/1:160,90:250:99:1245,0,2300	0/1:156,81:238:99:724,0,2764
+chr22	42523077	.	A	G	54.31	.	AC=1;AF=0.071;AN=14;BaseQRankSum=-0.563;DP=1521;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=54.8434;MQ=164.04;MQ0=1;MQRankSum=-2.419;QD=2.59;ReadPosRankSum=-1.229	GT:AD:DP:GQ:PL	0/1:17,4:21:92.74:93,0,533	0/0:249,1:250:99:0,544,6985	0/0:250,0:250:99:0,577,6968	0/0:248,2:250:99:0,605,7687	0/0:248,1:249:99:0,583,7300	0/0:246,2:249:99:0,626,7473	0/0:248,1:249:99:0,594,7553
+chr22	42523209	rs28371730	T	C	15556.89	.	AC=8;AF=0.571;AN=14;BaseQRankSum=3.458;DB;DP=1509;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=120.8206;MQ=221.07;MQ0=0;MQRankSum=-4.945;QD=10.31;ReadPosRankSum=0.639	GT:AD:DP:GQ:PL	0/1:3,6:9:99:154,0,101	1/1:6,237:247:99:4532,308,0	0/1:130,117:248:99:1399,0,3147	0/1:112,129:244:99:2641,0,2556	0/1:115,127:247:99:2320,0,2526	0/1:115,128:248:99:2546,0,2520	0/1:143,104:249:99:1965,0,3288
+chr22	42523211	rs2004511	T	C	2445.52	.	AC=2;AF=0.143;AN=14;BaseQRankSum=10.587;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=102.7564;MQ=221.50;MQ0=0;MQRankSum=-6.926;QD=4.89;ReadPosRankSum=2.057	GT:AD:DP:GQ:PL	0/0:9,0:9:24.06:0,24,289	0/1:136,113:250:99:1384,0,2176	0/1:146,104:250:99:1108,0,2809	0/0:247,3:250:99:0,439,5546	0/0:245,2:249:99:0,459,5316	0/0:248,2:250:99:0,459,5404	0/0:248,1:250:99:0,533,6069
+chr22	42523409	rs1985842	G	T	6801.90	.	AC=6;AF=0.429;AN=14;BaseQRankSum=20.509;DB;DP=1454;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=150.8967;MQ=200.12;MQ0=0;MQRankSum=4.472;QD=5.65;ReadPosRankSum=9.396	GT:AD:DP:GQ:PL	0/1:1,3:4:25.84:53,0,26	0/1:153,95:249:99:1597,0,1798	0/0:245,4:250:99:0,336,4079	0/1:168,82:250:99:1339,0,1880	0/1:147,103:250:99:1522,0,1805	0/1:156,94:250:99:1341,0,2322	0/1:129,71:201:99:949,0,2082
+chr22	42523805	rs28371725	C	T	1637.33	.	AC=1;AF=0.071;AN=14;BaseQRankSum=-0.379;DB;DP=1516;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=77.2321;MQ=226.05;MQ0=0;MQRankSum=2.862;QD=6.55;ReadPosRankSum=0.064	GT:AD:DP:GQ:PL	0/0:16,0:16:39.09:0,39,475	0/0:248,1:249:99:0,613,7187	0/1:132,116:248:99:1676,0,2916	0/0:248,0:248:99:0,625,7171	0/0:248,2:250:99:0,604,7252	0/0:250,0:250:99:0,631,7426	0/0:248,1:249:99:0,584,6964
+chr22	42523943	rs16947	A	G	23661.10	.	AC=8;AF=0.571;AN=14;BaseQRankSum=4.602;DB;DP=1514;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=38.3217;MQ=238.64;MQ0=0;MQRankSum=2.485;QD=15.63;ReadPosRankSum=3.749	GT:AD:DP:GQ:PL	0/1:9,5:14:99:163,0,303	1/1:3,246:250:99:8092,667,0	0/1:129,116:246:99:3190,0,2852	0/1:149,98:247:99:2429,0,3588	0/1:129,118:247:99:3267,0,3052	0/1:122,123:245:99:3428,0,3052	0/1:124,119:244:99:3092,0,2845
+chr22	42524150	.	C	G	3758.65	.	AC=8;AF=0.571;AN=14;BaseQRankSum=24.314;DP=1506;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=172.5901;MQ=242.92;MQ0=0;MQRankSum=11.537;QD=2.50;ReadPosRankSum=-9.185	GT:AD:DP:GQ:PL	1/1:3,3:6:5.98:46,6,0	0/1:161,88:250:99:708,0,300	0/1:161,88:250:99:635,0,308	0/1:160,90:250:99:658,0,229	0/1:180,69:250:99:478,0,113	0/1:176,73:250:99:530,0,271	0/1:170,79:249:99:704,0,133
+chr22	42524435	rs1807313	T	A	5252.25	.	AC=3;AF=0.214;AN=14;BaseQRankSum=-0.192;DB;DP=1526;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=152.3866;MQ=242.06;MQ0=0;MQRankSum=1.923;QD=9.99;ReadPosRankSum=3.008	GT:AD:DP:GQ:PL	0/1:7,19:26:99:456,0,195	0/0:250,0:250:99:0,698,8167	0/0:246,2:249:99:0,673,7735	0/0:248,2:250:99:0,685,7919	0/0:250,0:250:99:0,688,7814	0/1:120,126:247:99:2539,0,3250	0/1:131,110:246:99:2257,0,3278
+chr22	42524696	rs58440431	T	C	6423.61	.	AC=2;AF=0.143;AN=14;BaseQRankSum=3.119;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=53.0005;MQ=230.78;MQ0=0;MQRankSum=2.825;QD=12.85;ReadPosRankSum=2.051	GT:AD:DP:GQ:PL	0/0:9,0:9:27.08:0,27,351	0/1:132,116:250:99:3341,0,3914	0/1:141,108:250:99:3082,0,3917	0/0:248,1:250:99:0,692,8578	0/0:250,0:250:99:0,743,8836	0/0:247,2:250:99:0,695,8726	0/0:249,1:250:99:0,699,8650
+chr22	42524947	rs3892097	C	T	731.18	.	AC=2;AF=0.143;AN=14;BaseQRankSum=0.602;DB;DP=1495;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=154.5421;MQ=217.65;MQ0=0;MQRankSum=4.304;QD=1.47;ReadPosRankSum=1.019	GT:AD:DP:GQ:PL	0/0:3,0:3:8.99:0,9,89	0/1:108,75:244:99:403,0,1684	0/1:125,74:242:99:375,0,2335	0/0:227,1:249:99:0,460,5036	0/0:226,1:247:99:0,448,4884	0/0:192,1:247:99:0,400,4405	0/0:194,1:247:99:0,405,4694
+chr22	42525132	rs1058164	G	C	14639.91	.	AC=5;AF=0.357;AN=14;BaseQRankSum=4.944;DB;DP=1508;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=38.1229;MQ=207.02;MQ0=6;MQRankSum=2.510;QD=11.71;ReadPosRankSum=0.306	GT:AD:DP:GQ:PL	0/0:8,0:8:24.05:0,24,309	0/1:125,125:250:99:3147,0,3294	0/0:245,1:248:99:0,549,7172	0/1:139,109:248:99:2470,0,3232	0/1:136,107:243:99:2545,0,3408	0/1:116,130:247:99:3206,0,2926	0/1:122,124:247:99:3271,0,3300
+chr22	42525772	rs28371706	G	A	7552.52	.	AC=4;AF=0.286;AN=14;BaseQRankSum=12.028;DB;DP=1506;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=89.8512;MQ=222.09;MQ0=0;MQRankSum=5.200;QD=9.99;ReadPosRankSum=2.275	GT:AD:DP:GQ:PL	0/1:4,2:6:29.34:29,0,147	0/0:249,0:249:99:0,592,6835	0/0:249,1:250:99:0,590,7041	0/0:248,0:248:99:0,652,7316	0/1:126,120:248:99:2668,0,2833	0/1:134,113:247:99:2453,0,2485	0/1:137,113:250:99:2403,0,2988
+chr22	42525798	rs28371705	G	C	1954.58	.	AC=2;AF=0.143;AN=14;BaseQRankSum=6.229;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=36.0442;MQ=228.55;MQ0=0;MQRankSum=0.852;QD=3.91;ReadPosRankSum=6.520	GT:AD:DP:GQ:PL	0/0:9,0:9:27.08:0,27,342	0/1:164,85:250:99:981,0,3519	0/1:171,79:250:99:1020,0,3665	0/0:249,1:250:99:0,526,6474	0/0:249,1:250:99:0,550,6481	0/0:248,2:250:99:0,542,6933	0/0:250,0:250:99:0,604,7282
+chr22	42525811	rs28371704	T	C	3688.26	.	AC=2;AF=0.143;AN=14;BaseQRankSum=4.752;DB;DP=1510;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=36.9902;MQ=210.28;MQ0=0;MQRankSum=2.309;QD=7.38;ReadPosRankSum=6.262	GT:AD:DP:GQ:PL	0/0:10,0:10:27.06:0,27,333	0/1:163,86:249:99:1958,0,3391	0/1:167,78:245:99:1730,0,3945	0/0:248,1:249:99:0,542,6887	0/0:246,1:247:99:0,550,6569	0/0:247,1:250:99:0,548,6954	0/0:249,1:250:99:0,557,7079
+chr22	42525821	rs28371703	G	T	3940.90	.	AC=2;AF=0.143;AN=14;BaseQRankSum=4.652;DB;DP=1510;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=34.0483;MQ=210.28;MQ0=0;MQRankSum=2.924;QD=7.88;ReadPosRankSum=5.487	GT:AD:DP:GQ:PL	0/0:10,0:10:24.08:0,24,317	0/1:164,85:250:99:2033,0,3659	0/1:167,79:249:99:1907,0,4271	0/0:249,1:250:99:0,565,7321	0/0:249,1:250:99:0,545,7102	0/0:248,2:250:99:0,536,7254	0/0:249,0:250:99:0,605,7633
+chr22	42525952	rs71328650	C	A	5872.92	.	AC=7;AF=0.500;AN=14;BaseQRankSum=25.986;DB;DP=1505;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=144.2979;MQ=173.55;MQ0=0;MQRankSum=3.660;QD=4.68;ReadPosRankSum=7.152	GT:AD:DP:GQ:PL	1/1:2,3:5:6:53,6,0	0/1:132,117:250:99:1397,0,702	0/0:248,1:250:99:0,245,2219	0/1:166,83:250:99:1151,0,934	0/1:164,86:250:99:1070,0,1147	0/1:170,80:250:99:1009,0,1141	0/1:162,87:250:99:1194,0,1085
+chr22	42526049	.	C	G	8544.41	.	AC=10;AF=0.714;AN=14;BaseQRankSum=-8.121;DP=1505;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=241.7335;MQ=162.18;MQ0=2;MQRankSum=-1.399;QD=6.81;ReadPosRankSum=2.132	GT:AD:DP:GQ:PL	1/1:0,5:5:3:26,3,0	0/1:86,162:248:99:1053,0,1167	0/0:235,12:248:99:0,378,3886	0/1:108,137:245:99:782,0,1662	1/1:3,242:245:99:2351,264,0	1/1:5,245:250:99:2193,222,0	1/1:4,242:246:99:2140,240,0
+chr22	42526449	.	T	A	151.47	.	AC=1;AF=0.071;AN=14;BaseQRankSum=2.662;DP=1226;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=41.2083;MQ=240.47;MQ0=0;MQRankSum=0.578;QD=4.89;ReadPosRankSum=3.611	GT:AD:DP:GQ:PL	0/1:23,8:31:99:190,0,694	0/0:188,0:190:99:0,478,5376	0/0:187,0:187:99:0,493,5322	0/0:247,0:249:99:0,634,6728	0/0:185,0:185:99:0,487,5515	0/0:202,0:202:99:0,520,5857	0/0:181,1:182:99:0,440,5362
+chr22	42526484	rs28371699	A	C	4220.99	.	AC=6;AF=0.429;AN=14;BaseQRankSum=-17.855;DB;DP=1532;DS;Dels=0.02;FS=0.000;HRun=0;HaplotypeScore=136.8893;MQ=233.92;MQ0=0;MQRankSum=3.448;QD=3.29;ReadPosRankSum=-2.663	GT:AD:DP:GQ:PL	0/1:16,15:31:99:238,0,428	0/1:112,135:247:99:796,0,1908	0/0:227,13:241:99:0,433,4747	0/1:108,133:242:99:588,0,2014	0/1:90,154:245:99:1055,0,1892	0/1:112,131:246:99:741,0,2222	0/1:108,137:246:99:803,0,2266
+chr22	42526549	rs56011157	C	T	14276.31	.	AC=8;AF=0.571;AN=14;BaseQRankSum=17.750;DB;DP=1537;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=87.3394;MQ=231.34;MQ0=0;MQRankSum=4.781;QD=9.29;ReadPosRankSum=7.463	GT:AD:DP:GQ:PL	0/1:22,15:37:99:251,0,330	1/1:23,227:250:99:5404,430,0	0/1:151,98:250:99:1878,0,2475	0/1:153,97:250:99:1769,0,2410	0/1:149,100:250:99:1792,0,2569	0/1:164,84:250:99:1440,0,2646	0/1:149,98:248:99:1742,0,2601
+chr22	42526561	rs28695233	G	T	4524.61	.	AC=7;AF=0.500;AN=14;BaseQRankSum=9.714;DB;DP=1538;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=98.8415;MQ=220.45;MQ0=0;MQRankSum=9.430;QD=3.02;ReadPosRankSum=7.682	GT:AD:DP:GQ:PL	0/0:22,15:38:15.74:0,16,609	1/1:4,240:249:99:2685,237,0	0/1:142,108:250:99:505,0,3133	0/1:138,109:249:99:521,0,3281	0/1:150,99:249:99:336,0,3601	0/1:153,93:250:99:194,0,3695	0/1:148,97:249:99:283,0,3093
+chr22	42526562	rs75276289	G	C	3780.51	.	AC=6;AF=0.429;AN=14;BaseQRankSum=15.200;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=116.4370;MQ=215.67;MQ0=0;MQRankSum=9.072;QD=2.52;ReadPosRankSum=10.863	GT:AD:DP:GQ:PL	0/0:25,15:40:17.73:0,18,633	0/1:50,199:250:99:1522,0,283	0/1:143,106:250:99:600,0,2844	0/1:143,107:250:99:605,0,3002	0/1:151,99:250:99:432,0,3352	0/1:157,93:250:99:254,0,3483	0/1:149,99:248:99:368,0,2999
+chr22	42526567	rs76312385	G	A	434.33	.	AC=1;AF=0.071;AN=14;BaseQRankSum=18.089;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=89.3746;MQ=219.80;MQ0=0;MQRankSum=6.196;QD=1.74;ReadPosRankSum=7.564	GT:AD:DP:GQ:PL	0/0:22,18:40:4.68:0,5,427	0/1:34,215:250:56.26:473,0,56	0/0:142,108:250:20.78:0,21,2288	0/0:142,108:250:49.48:0,49,2451	0/0:152,97:250:99:0,210,2801	0/0:150,100:250:34.96:0,35,2515	0/0:148,102:250:77.19:0,77,2590
+chr22	42526571	rs74644586	C	G	339.60	.	AC=1;AF=0.071;AN=14;BaseQRankSum=-11.480;DB;DP=1540;DS;Dels=0.02;FS=0.000;HRun=4;HaplotypeScore=93.3402;MQ=218.52;MQ0=0;MQRankSum=3.709;QD=1.36;ReadPosRankSum=6.322	GT:AD:DP:GQ:PL	0/0:22,18:40:36.46:0,36,689	0/1:4,232:239:30.49:378,0,30	0/0:138,110:249:99:0,295,4017	0/0:137,111:249:99:0,250,4041	0/0:147,97:245:99:0,321,4348	0/0:150,97:247:99:0,358,4657	0/0:144,101:247:99:0,275,4123
+chr22	42526573	rs1080996	T	G	12579.34	.	AC=8;AF=0.571;AN=14;BaseQRankSum=6.163;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=76.6550;MQ=224.49;MQ0=0;MQRankSum=1.355;QD=8.17;ReadPosRankSum=5.794	GT:AD:DP:GQ:PL	0/1:22,18:40:99:200,0,668	1/1:4,244:248:99:5175,439,0	0/1:136,110:250:99:1862,0,3521	0/1:136,113:249:99:1734,0,3677	0/1:144,99:250:99:1119,0,3818	0/1:150,99:250:99:1196,0,4178	0/1:145,104:250:99:1293,0,3628
+chr22	42526580	rs1080995	G	C	16619.47	.	AC=8;AF=0.571;AN=14;BaseQRankSum=7.991;DB;DP=1541;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=56.1489;MQ=221.29;MQ0=0;MQRankSum=2.223;QD=10.78;ReadPosRankSum=4.443	GT:AD:DP:GQ:PL	0/1:22,19:41:99:335,0,664	1/1:15,234:250:99:5895,337,0	0/1:137,113:250:99:2421,0,3301	0/1:134,116:250:99:2262,0,3430	0/1:144,105:250:99:1929,0,3421	0/1:148,101:250:99:1778,0,3867	0/1:142,108:250:99:1999,0,3334
+chr22	42526634	.	T	C	32.60	.	AC=1;AF=0.071;AN=14;BaseQRankSum=1.147;DP=1225;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=50.0151;MQ=240.65;MQ0=0;MQRankSum=1.151;QD=1.30;ReadPosRankSum=1.276	GT:AD:DP:GQ:PL	0/1:21,4:25:71.04:71,0,702	0/0:187,2:189:99:0,481,6080	0/0:233,0:233:99:0,667,7351	0/0:230,0:230:99:0,667,7394	0/0:174,1:175:99:0,446,5469	0/0:194,2:196:99:0,498,6239	0/0:174,0:175:99:0,511,5894
+chr22	42526679	.	G	C	60.60	.	AC=1;AF=0.071;AN=14;BaseQRankSum=-12.425;DP=1525;DS;Dels=0.09;FS=0.000;HRun=1;HaplotypeScore=331.3182;MQ=215.48;MQ0=0;MQRankSum=-14.680;QD=0.24;ReadPosRankSum=-13.323	GT:AD:DP:GQ:PL	0/0:23,0:23:66.17:0,66,829	0/1:175,56:232:99:99,0,4273	0/0:199,26:226:76.45:0,76,5104	0/0:196,37:233:41.98:0,42,5109	0/0:170,47:218:99:0,162,4505	0/0:188,36:224:99:0,230,4974	0/0:177,47:225:99:0,167,4592
+chr22	42526694	rs1065852	G	A	4420.63	.	AC=2;AF=0.143;AN=14;BaseQRankSum=8.566;DB;DP=1529;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=117.6833;MQ=214.96;MQ0=0;MQRankSum=5.852;QD=8.84;ReadPosRankSum=1.454	GT:AD:DP:GQ:PL	0/0:29,0:29:81.24:0,81,1040	0/1:136,114:250:99:2333,0,3170	0/1:145,104:250:99:2087,0,2794	0/0:250,0:250:99:0,586,6963	0/0:247,2:250:99:0,497,6185	0/0:248,2:250:99:0,544,6640	0/0:250,0:250:99:0,571,6444
+chr22	42527471	rs28633410	T	C	26831.16	.	AC=10;AF=0.833;AN=12;BaseQRankSum=-1.092;DB;DP=1501;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=79.3853;MQ=176.86;MQ0=0;MQRankSum=-2.644;QD=17.89;ReadPosRankSum=2.185	GT:AD:DP:GQ:PL	./.	1/1:1,249:250:99:5741,478,0	0/1:102,148:250:99:3026,0,1748	0/1:115,132:250:99:2716,0,1896	1/1:1,249:250:99:5040,392,0	1/1:1,248:250:99:5109,427,0	1/1:4,245:249:99:5199,306,0
+chr22	42527533	rs28624811	A	G	13619.46	.	AC=7;AF=0.583;AN=12;BaseQRankSum=-8.893;DB;DP=1501;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=86.1948;MQ=179.18;MQ0=0;MQRankSum=0.472;QD=9.08;ReadPosRankSum=0.778	GT:AD:DP:GQ:PL	./.	1/1:2,241:243:99:4171,416,0	0/1:113,132:245:99:2000,0,2018	0/1:120,126:246:99:1781,0,1970	0/1:131,118:249:99:1885,0,1784	0/1:122,126:248:99:1893,0,1807	0/1:122,127:249:99:1890,0,2119
+chr22	42527793	rs1080989	C	T	3454.66	.	AC=2;AF=0.167;AN=12;BaseQRankSum=-3.007;DB;DP=1074;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=75.7865;MQ=209.00;MQ0=0;MQRankSum=3.014;QD=9.36;ReadPosRankSum=0.618	GT:AD:DP:GQ:PL	./.	0/1:72,90:162:99:1699,0,1767	0/1:103,96:202:99:1756,0,2532	0/0:188,0:188:99:0,526,5889	0/0:160,0:160:99:0,457,4983	0/0:197,0:198:99:0,544,6100	0/0:156,0:156:99:0,439,5041
+chr22	42527891	.	T	A	109.83	.	AC=5;AF=0.417;AN=12;BaseQRankSum=11.235;DP=1500;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=638.4601;MQ=166.82;MQ0=0;MQRankSum=1.444;QD=0.09;ReadPosRankSum=0.839	GT:AD:DP:GQ:PL	./.	0/1:238,7:248:13.70:14,0,38	0/0:246,3:250:5.97:0,6,45	0/1:239,11:250:31.42:31,0,54	0/1:232,16:250:49.09:49,0,76	0/1:233,14:249:52.10:52,0,53	0/1:238,11:250:12.71:13,0,36

From b956aa2542c4762c1e6e15315f7a050a84988b65 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 11:04:29 +0200
Subject: [PATCH 11/31] Updated readme.md

---
 README.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/README.md b/README.md
index 2a45874..0a64126 100644
--- a/README.md
+++ b/README.md
@@ -190,4 +190,16 @@ An API key is required in order to batch requests or enable allele frequency fil
 
 To obtain an API key please [contact us](mailto:support@saphetor.com)
 
+### How to run the tests
+
+Clone the repository after creating a virtual environment, and run
+
+    python setup.py test
+    
+In order to run the tests it is advised that you set the VARIANT_API_KEY env var to your api token,
+otherwise several tests will fail because the API will return a 429 (too many requests error).
+Be advised as well that running the tests will count towards your account request limit depending on the
+API package you are subscribed to.
+ 
+
 

From b5fb6efda3a5c549aaa5e3ab541fa04a5ac4598f Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 11:27:59 +0200
Subject: [PATCH 12/31] API-106 #comment finalized client. Writter unittests,
 updated doc, rename to varsome-api-client

---
 README.md                                     | 42 +++++++++----------
 ...ate_vcf.py => varsome_api_annotate_vcf.py} |  2 +-
 .../{variantapi_run.py => varsome_api_run.py} |  4 +-
 setup.py                                      |  6 +--
 {variantapi => varsome_api}/__init__.py       |  0
 {variantapi => varsome_api}/client.py         | 24 +++++------
 .../models/__init__.py                        |  0
 .../models/elements/__init__.py               |  0
 .../models/elements/broad.py                  |  0
 .../models/elements/dann.py                   |  0
 .../models/elements/dbnsfp.py                 |  0
 .../models/elements/gerp.py                   |  0
 .../models/elements/gnomad.py                 |  0
 .../models/elements/gwas.py                   |  0
 .../models/elements/iarc.py                   |  0
 .../models/elements/icgc.py                   |  0
 .../models/elements/isb.py                    |  0
 .../models/elements/ncbi.py                   |  2 +-
 .../models/elements/sanger.py                 |  0
 .../models/elements/thousand_genomes.py       |  0
 .../models/elements/transcript.py             |  0
 .../models/elements/uniprot.py                |  0
 .../models/elements/wustl.py                  |  0
 {variantapi => varsome_api}/models/fields.py  |  0
 {variantapi => varsome_api}/models/variant.py |  0
 {variantapi => varsome_api}/tests/__init__.py |  0
 .../tests/test_client.py                      | 16 +++----
 .../tests/variants.csv                        |  0
 .../tests/variants.vcf                        |  0
 {variantapi => varsome_api}/vcf.py            |  6 +--
 30 files changed, 51 insertions(+), 51 deletions(-)
 rename scripts/{variantapi_annotate_vcf.py => varsome_api_annotate_vcf.py} (97%)
 rename scripts/{variantapi_run.py => varsome_api_run.py} (98%)
 rename {variantapi => varsome_api}/__init__.py (100%)
 rename {variantapi => varsome_api}/client.py (91%)
 rename {variantapi => varsome_api}/models/__init__.py (100%)
 rename {variantapi => varsome_api}/models/elements/__init__.py (100%)
 rename {variantapi => varsome_api}/models/elements/broad.py (100%)
 rename {variantapi => varsome_api}/models/elements/dann.py (100%)
 rename {variantapi => varsome_api}/models/elements/dbnsfp.py (100%)
 rename {variantapi => varsome_api}/models/elements/gerp.py (100%)
 rename {variantapi => varsome_api}/models/elements/gnomad.py (100%)
 rename {variantapi => varsome_api}/models/elements/gwas.py (100%)
 rename {variantapi => varsome_api}/models/elements/iarc.py (100%)
 rename {variantapi => varsome_api}/models/elements/icgc.py (100%)
 rename {variantapi => varsome_api}/models/elements/isb.py (100%)
 rename {variantapi => varsome_api}/models/elements/ncbi.py (98%)
 rename {variantapi => varsome_api}/models/elements/sanger.py (100%)
 rename {variantapi => varsome_api}/models/elements/thousand_genomes.py (100%)
 rename {variantapi => varsome_api}/models/elements/transcript.py (100%)
 rename {variantapi => varsome_api}/models/elements/uniprot.py (100%)
 rename {variantapi => varsome_api}/models/elements/wustl.py (100%)
 rename {variantapi => varsome_api}/models/fields.py (100%)
 rename {variantapi => varsome_api}/models/variant.py (100%)
 rename {variantapi => varsome_api}/tests/__init__.py (100%)
 rename {variantapi => varsome_api}/tests/test_client.py (92%)
 rename {variantapi => varsome_api}/tests/variants.csv (100%)
 rename {variantapi => varsome_api}/tests/variants.vcf (100%)
 rename {variantapi => varsome_api}/vcf.py (97%)

diff --git a/README.md b/README.md
index 0a64126..cf89d5c 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Variant API Client
+# VarSome API Client
 
 ## A basic api client implementation for [api.varsome.com](https://api.varsome.com)
 
@@ -23,27 +23,27 @@ Activate the virtual environment
     source venv_dir_name/bin/activate
 
 
-Finally to use the client either download or clone the repository from github and place the variantapi package
+Finally to use the client either download or clone the repository from github and place the varsome_api package
 within your code, or do
 
-    pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
+    pip install https://github.com/saphetor/varsome-api-client-python/archive/master.zip
 
-The client will be installed within your virtual environment. Also 2 scripts called variantapi_run.py and 
-variantapi_annotate_vcf.py will be available within your virtual environment $PATH
+The client will be installed within your virtual environment. Also 2 scripts called varsome_api_run.py and 
+varsome_api_annotate_vcf.py will be available within your virtual environment $PATH
 
 ### Using the scripts to directly annotate a list of variants or a vcf file
 
 #### Annotating a variant or list of variants
 Try the following query to annotate a single variant:
 
-    variantapi_run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
+    varsome_api_run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
 
 The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensemble_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
 The script may also accept a txt file with variants (one per line) and an optional output file to store the
 annotations to. It is advised that you don't use this script with a large number of variants but directly use
 the client within your code.
 
-    variantapi_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1
+    varsome_api_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1
     
 Will read variants from variants.txt and dump the annotations to annotations.txt. If you don't use the -k
 parameter the script will do as many requests as the variants within variants.txt file and you will probably
@@ -52,7 +52,7 @@ end up with HTTP status code 429 (Too many requests) error.
 #### Annotating a vcf file
 To annotate a vcf file use:
 
-    variantapi_annotate_vcf.py -g hg19 -k api_key -i input.vcf -o annotated_vcf.vcf -p add-all-data=1
+    varsome_api_annotate_vcf.py -g hg19 -k api_key -i input.vcf -o annotated_vcf.vcf -p add-all-data=1
     
 Notice however that not all available annotations will be present in the annotated_vcf file. Only a subset
 of the returned annotations will be available, when running this script. Have a look at "Using the client in your code" 
@@ -63,12 +63,12 @@ section on how to annotate a vcf file with the annotations that are of interest
 Using the api client is quite straightforward. Just install the api client package and from within
 your code use
 
-    from variantapi.client import VariantAPIClient
+    from varsome_api.client import VarSomeAPIClient
     # api key is not required for single variant lookups
     api_key = 'Your token'
-    api = VariantAPIClient(api_key)
+    api = VarSomeAPIClient(api_key)
     # if you don't have an api key use
-    # api = VariantAPIClient()
+    # api = VarSomeAPIClient()
     # fetch information about a variant into a dictionary
     result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
     # access results e.g. the transcripts of the variant
@@ -82,11 +82,11 @@ your code use
 If errors occur while using the client an exception will be thrown.
 You may wish to catch this exception and proceed with your own code logic
 
-    from variantapi.client import VariantAPIClient, VariantApiException
-    api = VariantAPIClient()
+    from varsome_api.client import VarSomeAPIClient, VarSomeAPIException
+    api = VarSomeAPIClient()
     try:
        result = api.lookup('chr19:20082943:1:G', ref_genome='hg64')
-    except VariantApiException as e:
+    except VarSomeAPIException as e:
         # proceed with your code flow e.g.
         print(e) # 404 (invalid reference genome)
 
@@ -99,11 +99,11 @@ To understand how annotation properties are included in the json response please
 If you don't want to read through each attribute in the json response you can wrap the result into a Python
 [json model](http://jsonmodels.readthedocs.io/en/latest/readme.html).
 
-    from variantapi.client import VariantAPIClient
-    from variantapi.models.variant import AnnotatedVariant
+    from varsome_api.client import VarSomeAPIClient
+    from varsome_api.models.variant import AnnotatedVariant
     # api key is not required for single variant lookups
     api_key = 'Your token'
-    api = VariantAPIClient(api_key)
+    api = VarSomeAPIClient(api_key)
     # fetch information about a variant into a dictionary
     result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
     annotated_variant = AnnotatedVariant(**result)
@@ -136,7 +136,7 @@ to rewrite as:
 To annotate a vcf you can base your code on the VCFAnnotator object. This provides a basic implementation that
 will annotate a vcf file using a set of the available annotations. It uses [PyVCF](https://github.com/jamescasbon/PyVCF) to read and write to vcf files.
 
-    from variantapi.vcf import VCFAnnotator
+    from varsome_api.vcf import VCFAnnotator
     api_key = 'Your token'
     vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
     vcf_file = 'input.vcf'
@@ -146,7 +146,7 @@ will annotate a vcf file using a set of the available annotations. It uses [PyVC
 To annotate the vcf file with the annotations that you are interested in you need only override 2 methods
 in the VCFAnnotator class
 
-    from variantapi.vcf import VCFAnnotator
+    from varsome_api.vcf import VCFAnnotator
     from vcf.parser import _Info
     class MyVCFAnnotator(VCFAnnotator):
     
@@ -196,8 +196,8 @@ Clone the repository after creating a virtual environment, and run
 
     python setup.py test
     
-In order to run the tests it is advised that you set the VARIANT_API_KEY env var to your api token,
-otherwise several tests will fail because the API will return a 429 (too many requests error).
+In order to run the tests it is advised that you set the VARSOME_API_KEY env var to your api token,
+otherwise several tests will fail because the API will return a 429 (too many requests error) or 401 (Not authenticated).
 Be advised as well that running the tests will count towards your account request limit depending on the
 API package you are subscribed to.
  
diff --git a/scripts/variantapi_annotate_vcf.py b/scripts/varsome_api_annotate_vcf.py
similarity index 97%
rename from scripts/variantapi_annotate_vcf.py
rename to scripts/varsome_api_annotate_vcf.py
index e0fe770..7a90db4 100755
--- a/scripts/variantapi_annotate_vcf.py
+++ b/scripts/varsome_api_annotate_vcf.py
@@ -2,7 +2,7 @@
 import argparse
 import sys
 
-from variantapi.vcf import VCFAnnotator
+from varsome_api.vcf import VCFAnnotator
 
 __author__ = 'ckopanos'
 
diff --git a/scripts/variantapi_run.py b/scripts/varsome_api_run.py
similarity index 98%
rename from scripts/variantapi_run.py
rename to scripts/varsome_api_run.py
index a22e8b6..5164b5d 100755
--- a/scripts/variantapi_run.py
+++ b/scripts/varsome_api_run.py
@@ -4,7 +4,7 @@
 import sys
 import os
 
-from variantapi.client import VariantAPIClient
+from varsome_api.client import VarSomeAPIClient
 
 __author__ = 'ckopanos'
 
@@ -49,7 +49,7 @@ def annotate_variant(argv):
     request_parameters = None
     if args.p:
         request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
-    api = VariantAPIClient(api_key)
+    api = VarSomeAPIClient(api_key)
     if query:
         if len(query) == 1:
             result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome)
diff --git a/setup.py b/setup.py
index a0af3d0..1a01bc2 100755
--- a/setup.py
+++ b/setup.py
@@ -1,17 +1,17 @@
 from setuptools import setup, find_packages
 from os import path
 
-VERSION = (2, 0, '0b1')
+VERSION = (1, 0, '0b1')
 __version__ = VERSION
 __versionstr__ = '.'.join(map(str, VERSION))
 
 here = path.abspath(path.dirname(__file__))
 
 setup(
-    name='variant_api',
+    name='varsome_api_client',
     version=__versionstr__,
     packages=find_packages(".", ),
-    scripts=['scripts/variantapi_run.py', 'scripts/variantapi_annotate_vcf.py'],
+    scripts=['scripts/varsome_api_run.py', 'scripts/varsome_api_annotate_vcf.py'],
     url='https://github.com/saphetor/variant-api-client-python',
     license='Apache License, Version 2.0',
     test_suite='nose.collector',
diff --git a/variantapi/__init__.py b/varsome_api/__init__.py
similarity index 100%
rename from variantapi/__init__.py
rename to varsome_api/__init__.py
diff --git a/variantapi/client.py b/varsome_api/client.py
similarity index 91%
rename from variantapi/client.py
rename to varsome_api/client.py
index c680ee9..7d6c6f8 100755
--- a/variantapi/client.py
+++ b/varsome_api/client.py
@@ -7,7 +7,7 @@
 from requests.exceptions import HTTPError, Timeout, ConnectionError, RequestException
 
 
-class VariantApiException(Exception):
+class VarSomeAPIException(Exception):
     ERROR_CODES = {
         400: "Bad request. A parameter you have passed is not valid, or something in your request is wrong",
         401: "Not Authorized: either you need to provide authentication credentials, or the credentials provided aren't"
@@ -35,7 +35,7 @@ def __repr__(self):
         return "%s(status=%s)" % (self.__class__.__name__, self.status)
 
 
-class VariantAPIClientBase(object):
+class VarSomeAPIClientBase(object):
     _api_url = 'https://api.varsome.com'
     _accepted_methods = ('GET', 'POST')
 
@@ -59,7 +59,7 @@ def __init__(self, api_key=None, logger=None):
 
     def _make_request(self, path, method="GET", params=None, json_data=None):
         if method not in self._accepted_methods:
-            raise VariantApiException('', "Unsupported method %s" % method)
+            raise VarSomeAPIException('', "Unsupported method %s" % method)
         try:
             if method == "GET":
                 r = self.session.get(self._api_url + path, params=params, stream=True)
@@ -74,18 +74,18 @@ def _make_request(self, path, method="GET", params=None, json_data=None):
             return r
         except HTTPError as e:
             response = e.response
-            if response.status_code in VariantApiException.ERROR_CODES:
+            if response.status_code in VarSomeAPIException.ERROR_CODES:
                 error_message = "Unexpected error"
                 if r.headers['Content-Type'] == "application/json":
                     error_message = response.json().get("detail", None)
-                raise VariantApiException(response.status_code, error_message)
-            raise VariantApiException('', "Unknown http error %s" % e)
+                raise VarSomeAPIException(response.status_code, error_message)
+            raise VarSomeAPIException('', "Unknown http error %s" % e)
         except Timeout as e:
-            raise VariantApiException('', "Request timed out %s" % e)
+            raise VarSomeAPIException('', "Request timed out %s" % e)
         except ConnectionError as e:
-            raise VariantApiException('', "Connection failure or connection refused %s" % e)
+            raise VarSomeAPIException('', "Connection failure or connection refused %s" % e)
         except RequestException as e:
-            raise VariantApiException('', "Unknown error %s" % e)
+            raise VarSomeAPIException('', "Unknown error %s" % e)
 
     def get(self, path, params=None):
         response = self._make_request(path, "GET", params=params)
@@ -96,21 +96,21 @@ def post(self, path, params=None, json_data=None, raise_exceptions=True):
         try:
             response = self._make_request(path, "POST", params=params, json_data=json_data)
             return response.json()
-        except VariantApiException as e:
+        except VarSomeAPIException as e:
             if raise_exceptions:
                 raise e
             self.logger.error(e)
             return {'error': str(e)}
 
 
-class VariantAPIClient(VariantAPIClientBase):
+class VarSomeAPIClient(VarSomeAPIClientBase):
     schema_lookup_path = "/lookup/schema"
     lookup_path = "/lookup/%s"
     ref_genome_lookup_path = lookup_path + "/%s"
     batch_lookup_path = "/lookup/batch/%s"
 
     def __init__(self, api_key=None, max_variants_per_batch=200):
-        super(VariantAPIClient, self).__init__(api_key)
+        super(VarSomeAPIClient, self).__init__(api_key)
         self.max_variants_per_batch = max_variants_per_batch
 
 
diff --git a/variantapi/models/__init__.py b/varsome_api/models/__init__.py
similarity index 100%
rename from variantapi/models/__init__.py
rename to varsome_api/models/__init__.py
diff --git a/variantapi/models/elements/__init__.py b/varsome_api/models/elements/__init__.py
similarity index 100%
rename from variantapi/models/elements/__init__.py
rename to varsome_api/models/elements/__init__.py
diff --git a/variantapi/models/elements/broad.py b/varsome_api/models/elements/broad.py
similarity index 100%
rename from variantapi/models/elements/broad.py
rename to varsome_api/models/elements/broad.py
diff --git a/variantapi/models/elements/dann.py b/varsome_api/models/elements/dann.py
similarity index 100%
rename from variantapi/models/elements/dann.py
rename to varsome_api/models/elements/dann.py
diff --git a/variantapi/models/elements/dbnsfp.py b/varsome_api/models/elements/dbnsfp.py
similarity index 100%
rename from variantapi/models/elements/dbnsfp.py
rename to varsome_api/models/elements/dbnsfp.py
diff --git a/variantapi/models/elements/gerp.py b/varsome_api/models/elements/gerp.py
similarity index 100%
rename from variantapi/models/elements/gerp.py
rename to varsome_api/models/elements/gerp.py
diff --git a/variantapi/models/elements/gnomad.py b/varsome_api/models/elements/gnomad.py
similarity index 100%
rename from variantapi/models/elements/gnomad.py
rename to varsome_api/models/elements/gnomad.py
diff --git a/variantapi/models/elements/gwas.py b/varsome_api/models/elements/gwas.py
similarity index 100%
rename from variantapi/models/elements/gwas.py
rename to varsome_api/models/elements/gwas.py
diff --git a/variantapi/models/elements/iarc.py b/varsome_api/models/elements/iarc.py
similarity index 100%
rename from variantapi/models/elements/iarc.py
rename to varsome_api/models/elements/iarc.py
diff --git a/variantapi/models/elements/icgc.py b/varsome_api/models/elements/icgc.py
similarity index 100%
rename from variantapi/models/elements/icgc.py
rename to varsome_api/models/elements/icgc.py
diff --git a/variantapi/models/elements/isb.py b/varsome_api/models/elements/isb.py
similarity index 100%
rename from variantapi/models/elements/isb.py
rename to varsome_api/models/elements/isb.py
diff --git a/variantapi/models/elements/ncbi.py b/varsome_api/models/elements/ncbi.py
similarity index 98%
rename from variantapi/models/elements/ncbi.py
rename to varsome_api/models/elements/ncbi.py
index 8dcbb9f..62cc7a1 100755
--- a/variantapi/models/elements/ncbi.py
+++ b/varsome_api/models/elements/ncbi.py
@@ -1,6 +1,6 @@
 from jsonmodels import models, fields
 
-from variantapi.models.fields import DictField
+from varsome_api.models.fields import DictField
 
 __author__ = "ckopanos"
 
diff --git a/variantapi/models/elements/sanger.py b/varsome_api/models/elements/sanger.py
similarity index 100%
rename from variantapi/models/elements/sanger.py
rename to varsome_api/models/elements/sanger.py
diff --git a/variantapi/models/elements/thousand_genomes.py b/varsome_api/models/elements/thousand_genomes.py
similarity index 100%
rename from variantapi/models/elements/thousand_genomes.py
rename to varsome_api/models/elements/thousand_genomes.py
diff --git a/variantapi/models/elements/transcript.py b/varsome_api/models/elements/transcript.py
similarity index 100%
rename from variantapi/models/elements/transcript.py
rename to varsome_api/models/elements/transcript.py
diff --git a/variantapi/models/elements/uniprot.py b/varsome_api/models/elements/uniprot.py
similarity index 100%
rename from variantapi/models/elements/uniprot.py
rename to varsome_api/models/elements/uniprot.py
diff --git a/variantapi/models/elements/wustl.py b/varsome_api/models/elements/wustl.py
similarity index 100%
rename from variantapi/models/elements/wustl.py
rename to varsome_api/models/elements/wustl.py
diff --git a/variantapi/models/fields.py b/varsome_api/models/fields.py
similarity index 100%
rename from variantapi/models/fields.py
rename to varsome_api/models/fields.py
diff --git a/variantapi/models/variant.py b/varsome_api/models/variant.py
similarity index 100%
rename from variantapi/models/variant.py
rename to varsome_api/models/variant.py
diff --git a/variantapi/tests/__init__.py b/varsome_api/tests/__init__.py
similarity index 100%
rename from variantapi/tests/__init__.py
rename to varsome_api/tests/__init__.py
diff --git a/variantapi/tests/test_client.py b/varsome_api/tests/test_client.py
similarity index 92%
rename from variantapi/tests/test_client.py
rename to varsome_api/tests/test_client.py
index c968919..a308a72 100644
--- a/variantapi/tests/test_client.py
+++ b/varsome_api/tests/test_client.py
@@ -4,13 +4,13 @@
 
 import vcf
 from vcf.parser import _Info
-from variantapi.client import VariantAPIClient, VariantApiException
-from variantapi.models.variant import AnnotatedVariant
-from variantapi.vcf import VCFAnnotator
+from varsome_api.client import VarSomeAPIClient, VarSomeAPIException
+from varsome_api.models.variant import AnnotatedVariant
+from varsome_api.vcf import VCFAnnotator
 
 __author__ = "ckopanos"
 
-API_KEY = os.getenv('VARIANT_API_KEY', None)
+API_KEY = os.getenv('VARSOME_API_KEY', None)
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 VARIANTS_CSV_FILE = os.path.join(BASE_DIR, 'tests', 'variants.csv')
 VARIANTS_VCF_FILE = os.path.join(BASE_DIR, 'tests', 'variants.vcf')
@@ -20,7 +20,7 @@ class TestApiClient(unittest.TestCase):
 
     def __init__(self, methodName='runTest'):
         super().__init__(methodName)
-        self.client = VariantAPIClient(API_KEY)
+        self.client = VarSomeAPIClient(API_KEY)
         with open(VARIANTS_CSV_FILE) as f:
             self.variants_to_lookup = f.read().splitlines()
         if API_KEY is None:
@@ -37,8 +37,8 @@ def test_schema(self):
         self.assertIsNotNone(self.client.schema())
 
     def test_404(self):
-        """Check we can raise VariantApiException"""
-        with self.assertRaises(VariantApiException) as ve:
+        """Check we can raise VarSomeAPIException"""
+        with self.assertRaises(VarSomeAPIException) as ve:
             self.client.lookup('chrM:410:A:T', ref_genome='hg64')
         test_exception = ve.exception
         self.assertEqual(test_exception.status, 404)
@@ -64,7 +64,7 @@ class TestApiResponse(unittest.TestCase):
 
     def __init__(self, methodName='runTest'):
         super().__init__(methodName)
-        client = VariantAPIClient(API_KEY, max_variants_per_batch=1000)
+        client = VarSomeAPIClient(API_KEY, max_variants_per_batch=1000)
         with open(VARIANTS_CSV_FILE) as f:
             self.variants_to_lookup = f.read().splitlines()
         self.results = client.batch_lookup(self.variants_to_lookup, ref_genome='hg19',
diff --git a/variantapi/tests/variants.csv b/varsome_api/tests/variants.csv
similarity index 100%
rename from variantapi/tests/variants.csv
rename to varsome_api/tests/variants.csv
diff --git a/variantapi/tests/variants.vcf b/varsome_api/tests/variants.vcf
similarity index 100%
rename from variantapi/tests/variants.vcf
rename to varsome_api/tests/variants.vcf
diff --git a/variantapi/vcf.py b/varsome_api/vcf.py
similarity index 97%
rename from variantapi/vcf.py
rename to varsome_api/vcf.py
index 052ae06..9dbdd94 100755
--- a/variantapi/vcf.py
+++ b/varsome_api/vcf.py
@@ -3,13 +3,13 @@
 import vcf
 from collections import OrderedDict
 from vcf.parser import _Info
-from variantapi.client import VariantAPIClient
-from variantapi.models.variant import AnnotatedVariant
+from varsome_api.client import VarSomeAPIClient
+from varsome_api.models.variant import AnnotatedVariant
 
 __author__ = "ckopanos"
 
 
-class VCFAnnotator(VariantAPIClient):
+class VCFAnnotator(VarSomeAPIClient):
     """
     VCFAnnotator will take an input vcf file parse it and produce an annotated vcf file
     """

From 2bd13f3da335575bb0cc9059d27868116e8de37b Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 11:30:38 +0200
Subject: [PATCH 13/31] Updated readme

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cf89d5c..53fdd83 100644
--- a/README.md
+++ b/README.md
@@ -192,10 +192,11 @@ To obtain an API key please [contact us](mailto:support@saphetor.com)
 
 ### How to run the tests
 
-Clone the repository after creating a virtual environment, and run
+Clone the repository after creating a virtual environment, and run:
 
     python setup.py test
     
+Running the tests will install [nose](https://nose.readthedocs.io/en/latest/) in your virtual environment.
 In order to run the tests it is advised that you set the VARSOME_API_KEY env var to your api token,
 otherwise several tests will fail because the API will return a 429 (too many requests error) or 401 (Not authenticated).
 Be advised as well that running the tests will count towards your account request limit depending on the

From 4751bc4815f8c4d7b28fae36335d05fe06a81674 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 11:37:10 +0200
Subject: [PATCH 14/31] Updated readme

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 53fdd83..a300a86 100644
--- a/README.md
+++ b/README.md
@@ -157,6 +157,8 @@ in the VCFAnnotator class
             :return: annotated record object
             """
             record.INFO['gnomad_exomes_AN'] = variant_result.gnomad_exomes_an
+            # if you wish to also include the default annotations
+            # return super().annotate_record(record, variant_result)
             return record
         
             
@@ -168,6 +170,8 @@ in the VCFAnnotator class
             """
             vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer',
                                                                  'GnomAD exomes allele number value', None, None)
+            # if you wish to include also the default headers
+            # super().add_vcf_header_info(vcf_template)
                                                                  
     api_key = 'Your token'
     vcf_annotator = MyVCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})

From e68df2f6de05b1e86f8b03b84bfcdf3a3b81075a Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 11:54:21 +0200
Subject: [PATCH 15/31] Fixed typo in readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a300a86..4b3f33d 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ Try the following query to annotate a single variant:
 
     varsome_api_run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
 
-The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensemble_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
+The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensembl_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
 The script may also accept a txt file with variants (one per line) and an optional output file to store the
 annotations to. It is advised that you don't use this script with a large number of variants but directly use
 the client within your code.

From d1a35d759ab4308fc413046ee25049be81d1ec39 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 12:12:08 +0200
Subject: [PATCH 16/31] Updated setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1a01bc2..95efe7a 100755
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,7 @@
     version=__versionstr__,
     packages=find_packages(".", ),
     scripts=['scripts/varsome_api_run.py', 'scripts/varsome_api_annotate_vcf.py'],
-    url='https://github.com/saphetor/variant-api-client-python',
+    url='https://github.com/saphetor/varsome-api-client-python',
     license='Apache License, Version 2.0',
     test_suite='nose.collector',
     tests_require=['nose'],

From fc2c0912981d5278c5665c282be7318c2d0cd7d3 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 14:15:56 +0200
Subject: [PATCH 17/31] changed description in varsome_api_run

---
 scripts/varsome_api_run.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py
index 5164b5d..cb66e89 100755
--- a/scripts/varsome_api_run.py
+++ b/scripts/varsome_api_run.py
@@ -10,7 +10,7 @@
 
 
 def annotate_variant(argv):
-    parser = argparse.ArgumentParser(description='Sample Variant API calls')
+    parser = argparse.ArgumentParser(description='Sample VarSome API calls')
     parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
     parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
                         required=False, default='hg19')

From 793634e5aebee103a25249caedcf9472d3984f45 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 14:22:44 +0200
Subject: [PATCH 18/31] Removed clivar v1 from the client

---
 varsome_api/models/elements/ncbi.py | 18 ------------------
 varsome_api/models/variant.py       |  1 -
 2 files changed, 19 deletions(-)

diff --git a/varsome_api/models/elements/ncbi.py b/varsome_api/models/elements/ncbi.py
index 62cc7a1..4703287 100755
--- a/varsome_api/models/elements/ncbi.py
+++ b/varsome_api/models/elements/ncbi.py
@@ -10,24 +10,6 @@ class DbSNP(models.Base):
     rsid = fields.ListField(items_types=(int,), help_text="RS ID")
 
 
-class ClinVarDisease(models.Base):
-    clndbn = fields.StringField(help_text="Disease", required=False, nullable=True)
-    clnsig = fields.IntField(help_text="Clinical Significance", required=False, nullable=True)
-    databases = DictField(help_text="External links",
-                          required=False, )  # todo specify the types of databases and assorted values
-    clnsig_description = fields.StringField(help_text="Clinical Significance description", required=False,
-                                            nullable=True)
-
-
-class ClinVar(models.Base):
-    version = fields.StringField(help_text="Version")
-    clnorigin = fields.IntField(required=False, nullable=True, help_text="Allele Origin")
-    clnorigin_description = fields.StringField(help_text="Allele Origin description", required=False, nullable=True)
-    disease = fields.ListField(items_types=(ClinVarDisease,), help_text="Disease", nullable=True, required=False)
-    pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed references", required=False,
-                                          nullable=True)
-
-
 class ClinVar2(models.Base):
     version = fields.StringField(help_text="Version")
     review_status = fields.StringField(help_text="Review status", required=False, nullable=True)
diff --git a/varsome_api/models/variant.py b/varsome_api/models/variant.py
index 563eb08..2f1f584 100755
--- a/varsome_api/models/variant.py
+++ b/varsome_api/models/variant.py
@@ -35,7 +35,6 @@ class AnnotatedVariant(models.Base):
     sanger_cosmic = fields.ListField(required=False, items_types=(Cosmic,), help_text="Sanger Cosmic")
     sanger_cosmic_public = fields.ListField(required=False, items_types=(CosmicPublic,), help_text="Cosmic")
     sanger_cosmic_licensed = fields.ListField(required=False, items_types=(CosmicLicensed,), help_text="Cosmic")
-    ncbi_clinvar = fields.ListField(required=False, items_types=(ClinVar,), help_text="ClinVar")
     ncbi_clinvar2 = fields.ListField(required=False, items_types=(ClinVar2,), help_text="ClinVar2")
     icgc_somatic = fields.ListField(required=False, items_types=(Somatic,), help_text="ICGC Somatic")
     iarc_tp53_germline = fields.ListField(required=False, items_types=(TP53Germline,), help_text="IARC TP53 Germline")

From 7272f10b5c205b0b1e86ec9ea9246d7a95cd7e21 Mon Sep 17 00:00:00 2001
From: chapplec <charles.chapple@saphetor.com>
Date: Fri, 12 Jan 2018 13:42:04 +0100
Subject: [PATCH 19/31] Made some changes to the text of the rEADME file

---
 README.md | 105 +++++++++++++++++++++++++++---------------------------
 1 file changed, 52 insertions(+), 53 deletions(-)

diff --git a/README.md b/README.md
index 4b3f33d..be46b68 100644
--- a/README.md
+++ b/README.md
@@ -1,73 +1,72 @@
 # VarSome API Client
 
-## A basic api client implementation for [api.varsome.com](https://api.varsome.com)
+## A basic API client implementation for [api.varsome.com](https://api.varsome.com)
 
-This client is still in beta but it is a good start to start playing around with the API.
+This client is still in beta but it is a good for playing around with the API.
 
 ### Python versions
 Python version 3 is supported.
 
 ### Installation
-It is advised that you create a python virtual environment instead of globally installing the library
+We suggest that you create a python virtual environment instead of globally installing the library.
 
-There several ways to create a virtual environment but you can refer to [pip installation](https://pip.pypa.io/en/stable/installing/) and
+There are several ways to create a virtual environment, but you can refer to [pip installation](https://pip.pypa.io/en/stable/installing/) and
 [virtualenv installation](https://virtualenv.pypa.io/en/stable/installation/) to first install these 2 tools if you don't
 have them already installed via a package manager (Linux) or HomeBrew (MacOS), etc.
 
-To create a virtual env you can follow the [user guide](https://virtualenv.pypa.io/en/stable/userguide/) or simply run
+To create a virtual environment, you can follow the [user guide](https://virtualenv.pypa.io/en/stable/userguide/) or simply run:
 
     virtualenv -p path_to/python3 venv_dir_name
     
-Activate the virtual environment
+Activate the virtual environment:
 
     source venv_dir_name/bin/activate
 
 
-Finally to use the client either download or clone the repository from github and place the varsome_api package
-within your code, or do
+Finally, to use the client, either download or clone the repository from github and place the `varsome_api` 
+folder inside your project's directory, or run:
 
     pip install https://github.com/saphetor/varsome-api-client-python/archive/master.zip
 
-The client will be installed within your virtual environment. Also 2 scripts called varsome_api_run.py and 
-varsome_api_annotate_vcf.py will be available within your virtual environment $PATH
+The client will be installed within your virtual environment. Also, 2 scripts called `varsome_api_run.py` and 
+`varsome_api_annotate_vcf.py` will be available within your virtual environment's `$PATH`.
 
-### Using the scripts to directly annotate a list of variants or a vcf file
+### Using the scripts to directly annotate a list of variants or a VCF file
 
 #### Annotating a variant or list of variants
 Try the following query to annotate a single variant:
 
     varsome_api_run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1
 
-The script should complete without errors and display aprox 6,700 lines of data from dann, dbnsfp, ensembl_transcripts, gerp, gnomad_exomes, gnomad_exomes_coverage, icgc_somatic, ncbi_clinvar2, pub_med_articles, refseq_transcripts, sanger_cosmic_public, uniprot_variants, wustl_civic etc.
-The script may also accept a txt file with variants (one per line) and an optional output file to store the
-annotations to. It is advised that you don't use this script with a large number of variants but directly use
-the client within your code.
+The script should complete without errors and display aproximately 6,700 lines of data from `dann`, `dbnsfp`, `ensembl_transcripts`, `gerp`, `gnomad_exomes`, `gnomad_exomes_coverage`, `icgc_somatic`, `ncbi_clinvar2`, `pub_med_articles`, `refseq_transcripts`, `sanger_cosmic_public`, `uniprot_variants`, `wustl_civic` etc.
+The script can also accept a text file with variants (one per line) and an optional output file to store the
+annotations in. We suggest that you don't use this script for a large number of variants, but use
+the client within your code instead.
 
     varsome_api_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1
     
-Will read variants from variants.txt and dump the annotations to annotations.txt. If you don't use the -k
-parameter the script will do as many requests as the variants within variants.txt file and you will probably
-end up with HTTP status code 429 (Too many requests) error.
+The command above will read variants from `variants.txt` and dump the annotations to `annotations.txt`. 
+If you don't use the `-k` parameter, the script will do as many requests as there are variants in `variants.txt`,
+and you will probably get an HTTP status code 429 (too many requests) error.
 
-#### Annotating a vcf file
-To annotate a vcf file use:
+#### Annotating a VCF file
+To annotate a VCF file, use: 
 
     varsome_api_annotate_vcf.py -g hg19 -k api_key -i input.vcf -o annotated_vcf.vcf -p add-all-data=1
     
-Notice however that not all available annotations will be present in the annotated_vcf file. Only a subset
-of the returned annotations will be available, when running this script. Have a look at "Using the client in your code" 
-section on how to annotate a vcf file with the annotations that are of interest to you. 
+Notice, however, that not all available annotations will be present in the `annotated_vcf.vcf` file. Only a subset
+of the returned annotations will be available when running this script. See the "Using the client in your code" 
+section below for how to annotate a VCF file with the annotations that are of interest to you. 
 
 ### Using the client in your code
 
-Using the api client is quite straightforward. Just install the api client package and from within
-your code use
+Using the API client is quite straightforward. Just install the API client package and use the following in your code:
 
     from varsome_api.client import VarSomeAPIClient
-    # api key is not required for single variant lookups
+    # API key is not required for single variant lookups
     api_key = 'Your token'
     api = VarSomeAPIClient(api_key)
-    # if you don't have an api key use
+    # if you don't have an API key use
     # api = VarSomeAPIClient()
     # fetch information about a variant into a dictionary
     result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
@@ -75,12 +74,12 @@ your code use
     transcripts = result['refseq_transcripts']
     # fetch information for multiple variants
     variants = ['chr19:20082943:1:G','chr22:39777823::CAA']
-    # results will be an array of dictionaries an api key will be required for this request
+    # Results will be an array of dictionaries. An API key will be required for this request
     results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19')
     # look at the python doc for batch_lookup method for additional parameters
 
-If errors occur while using the client an exception will be thrown.
-You may wish to catch this exception and proceed with your own code logic
+If errors occur while using the client, an exception will be thrown.
+You may wish to catch this exception and proceed with your own code logic:
 
     from varsome_api.client import VarSomeAPIClient, VarSomeAPIException
     api = VarSomeAPIClient()
@@ -90,39 +89,39 @@ You may wish to catch this exception and proceed with your own code logic
         # proceed with your code flow e.g.
         print(e) # 404 (invalid reference genome)
 
-To view available request parameters (used in the params method parameter) refer to an example at [api.varsome.com](https://api.varsome.com)
+To view available request parameters (used by the `params` method parameter), refer to an example at [api.varsome.com](https://api.varsome.com).
 
-To understand how annotation properties are included in the json response please refer to the relevant [schema](https://api.varsome.com/lookup/schema)
+To understand how annotation properties are included in the JSON response, please refer to the relevant [schema](https://api.varsome.com/lookup/schema).
 
 #### JSON response wrapper
 
-If you don't want to read through each attribute in the json response you can wrap the result into a Python
-[json model](http://jsonmodels.readthedocs.io/en/latest/readme.html).
+If you don't want to read through each attribute in the JSON response, you can wrap the result into a Python
+[JSON model](http://jsonmodels.readthedocs.io/en/latest/readme.html):
 
     from varsome_api.client import VarSomeAPIClient
     from varsome_api.models.variant import AnnotatedVariant
-    # api key is not required for single variant lookups
+    # API key is not required for single variant lookups
     api_key = 'Your token'
     api = VarSomeAPIClient(api_key)
     # fetch information about a variant into a dictionary
     result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
     annotated_variant = AnnotatedVariant(**result)
 
-now you have access to a set of shortcut attributes (these will be updated over time in the code base)
+You now have access to a set of shortcut attributes (these will be updated over time in the code base):
 
     annotated_variant.chromosome
     annotated_variant.alt
     annotated_variant.genes # directly get the genes related to the variant
     annotated_variant.gnomad_exomes_af # etc
 
-or you may access other inner properties of other available properties
+Or you may access other inner properties of other available properties:
 
     # get gnomad exomes allele number
     allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes]
 
-annotated_variant.gnomad_exomes and also other json model type of objects that contain a version property, are
-always returned as lists of objects. This is because of the ability of the API to return multiple versions of 
-annotation databases (though this is not currently publicly available). For consistency reasons therefore
+JSON model-type objects that contain a `version` property, like `annotated_variant.gnomad_exomes`, are
+always returned as lists of objects. This is because the API has the ability to return multiple versions of 
+annotation databases (although this is not currently publicly available). For consistency, therefore,
 these are always lists, though it is safe to assume that they will only include a single item. So it is safe
 to rewrite as:
      
@@ -133,8 +132,8 @@ to rewrite as:
            
 #### Annotating a VCF using the client
 
-To annotate a vcf you can base your code on the VCFAnnotator object. This provides a basic implementation that
-will annotate a vcf file using a set of the available annotations. It uses [PyVCF](https://github.com/jamescasbon/PyVCF) to read and write to vcf files.
+To annotate a VCF you can base your code on the VCFAnnotator object. This provides a basic implementation that
+will annotate a VCF file using a set of the available annotations. It uses [PyVCF](https://github.com/jamescasbon/PyVCF) to read and write to VCF files.
 
     from varsome_api.vcf import VCFAnnotator
     api_key = 'Your token'
@@ -143,8 +142,8 @@ will annotate a vcf file using a set of the available annotations. It uses [PyVC
     output_vcf_file = 'annotated.vcf'
     vcf_annotator.annotate(vcf_file, output_vcf_file)
         
-To annotate the vcf file with the annotations that you are interested in you need only override 2 methods
-in the VCFAnnotator class
+To annotate the VCF file with the annotations that you are interested in, you need only override 2 methods
+(`annotate_record` and `add_vcf_header_info`) in the VCFAnnotator class:
 
     from varsome_api.vcf import VCFAnnotator
     from vcf.parser import _Info
@@ -170,7 +169,7 @@ in the VCFAnnotator class
             """
             vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer',
                                                                  'GnomAD exomes allele number value', None, None)
-            # if you wish to include also the default headers
+            # if you wish to also include the default headers
             # super().add_vcf_header_info(vcf_template)
                                                                  
     api_key = 'Your token'
@@ -182,27 +181,27 @@ in the VCFAnnotator class
         
 ### API Documentation
 
-Please visit the [api documentation](https://api.varsome.com) to find out how to use the api and
-what values does the api provide as a response to lookup requests
+See [API documentation](https://api.varsome.com) for information on how to use the API and
+what values the API provides as a response to lookup requests.
 
 ### How to get an API key
 
-You generally are not required to have an api key to use the api, though the number of requests you will be able
-to issue will be throttled if they exceed a certain number.
+You are generally not required to have an API key to use the API but, without one, the number of requests 
+you will be able to issue will be limited.
 
-An API key is required in order to batch requests or enable allele frequency filtering.
+You will also not be able to perform batch requests without an API key.
 
 To obtain an API key please [contact us](mailto:support@saphetor.com)
 
 ### How to run the tests
 
-Clone the repository after creating a virtual environment, and run:
+Clone the repository, after creating a virtual environment, and run:
 
     python setup.py test
     
 Running the tests will install [nose](https://nose.readthedocs.io/en/latest/) in your virtual environment.
-In order to run the tests it is advised that you set the VARSOME_API_KEY env var to your api token,
-otherwise several tests will fail because the API will return a 429 (too many requests error) or 401 (Not authenticated).
+To run the tests, set the `VARSOME_API_KEY` environment variable to your API token. Otherwise,
+several tests will fail because the API will return a 429 (too many requests) or 401 (not authenticated) error.
 Be advised as well that running the tests will count towards your account request limit depending on the
 API package you are subscribed to.
  

From 18649af0b8b25ac23ab1d8ec4d264f03a06c20c5 Mon Sep 17 00:00:00 2001
From: chapplec <charles.chapple@saphetor.com>
Date: Fri, 12 Jan 2018 15:40:23 +0100
Subject: [PATCH 20/31] added syntax highlighting to readme examples

---
 README.md | 176 +++++++++++++++++++++++++++++-------------------------
 1 file changed, 94 insertions(+), 82 deletions(-)

diff --git a/README.md b/README.md
index be46b68..dbf21a5 100644
--- a/README.md
+++ b/README.md
@@ -61,33 +61,35 @@ section below for how to annotate a VCF file with the annotations that are of in
 ### Using the client in your code
 
 Using the API client is quite straightforward. Just install the API client package and use the following in your code:
-
-    from varsome_api.client import VarSomeAPIClient
-    # API key is not required for single variant lookups
-    api_key = 'Your token'
-    api = VarSomeAPIClient(api_key)
-    # if you don't have an API key use
-    # api = VarSomeAPIClient()
-    # fetch information about a variant into a dictionary
-    result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
-    # access results e.g. the transcripts of the variant
-    transcripts = result['refseq_transcripts']
-    # fetch information for multiple variants
-    variants = ['chr19:20082943:1:G','chr22:39777823::CAA']
-    # Results will be an array of dictionaries. An API key will be required for this request
-    results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19')
-    # look at the python doc for batch_lookup method for additional parameters
-
+```python
+from varsome_api.client import VarSomeAPIClient
+# API key is not required for single variant lookups
+api_key = 'Your token'
+api = VarSomeAPIClient(api_key)
+# if you don't have an API key use
+# api = VarSomeAPIClient()
+# fetch information about a variant into a dictionary
+result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
+# access results e.g. the transcripts of the variant
+transcripts = result['refseq_transcripts']
+# fetch information for multiple variants
+variants = ['chr19:20082943:1:G','chr22:39777823::CAA']
+# Results will be an array of dictionaries. An API key will be required for this request
+results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19')
+# look at the python doc for batch_lookup method for additional parameters
+```
 If errors occur while using the client, an exception will be thrown.
 You may wish to catch this exception and proceed with your own code logic:
 
-    from varsome_api.client import VarSomeAPIClient, VarSomeAPIException
-    api = VarSomeAPIClient()
-    try:
-       result = api.lookup('chr19:20082943:1:G', ref_genome='hg64')
-    except VarSomeAPIException as e:
-        # proceed with your code flow e.g.
-        print(e) # 404 (invalid reference genome)
+```python
+from varsome_api.client import VarSomeAPIClient, VarSomeAPIException
+api = VarSomeAPIClient()
+try:
+   result = api.lookup('chr19:20082943:1:G', ref_genome='hg64')
+except VarSomeAPIException as e:
+    # proceed with your code flow e.g.
+    print(e) # 404 (invalid reference genome)
+```
 
 To view available request parameters (used by the `params` method parameter), refer to an example at [api.varsome.com](https://api.varsome.com).
 
@@ -98,86 +100,96 @@ To understand how annotation properties are included in the JSON response, pleas
 If you don't want to read through each attribute in the JSON response, you can wrap the result into a Python
 [JSON model](http://jsonmodels.readthedocs.io/en/latest/readme.html):
 
-    from varsome_api.client import VarSomeAPIClient
-    from varsome_api.models.variant import AnnotatedVariant
-    # API key is not required for single variant lookups
-    api_key = 'Your token'
-    api = VarSomeAPIClient(api_key)
-    # fetch information about a variant into a dictionary
-    result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
-    annotated_variant = AnnotatedVariant(**result)
+```python
+from varsome_api.client import VarSomeAPIClient
+from varsome_api.models.variant import AnnotatedVariant
+# API key is not required for single variant lookups
+api_key = 'Your token'
+api = VarSomeAPIClient(api_key)
+# fetch information about a variant into a dictionary
+result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
+annotated_variant = AnnotatedVariant(**result)
+```
 
 You now have access to a set of shortcut attributes (these will be updated over time in the code base):
 
-    annotated_variant.chromosome
-    annotated_variant.alt
-    annotated_variant.genes # directly get the genes related to the variant
-    annotated_variant.gnomad_exomes_af # etc
-
+```python
+annotated_variant.chromosome
+annotated_variant.alt
+annotated_variant.genes # directly get the genes related to the variant
+annotated_variant.gnomad_exomes_af # etc
+```
 Or you may access other inner properties of other available properties:
 
-    # get gnomad exomes allele number
-    allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes]
+```python
+# get gnomad exomes allele number
+allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes]
+```
 
 JSON model-type objects that contain a `version` property, like `annotated_variant.gnomad_exomes`, are
 always returned as lists of objects. This is because the API has the ability to return multiple versions of 
 annotation databases (although this is not currently publicly available). For consistency, therefore,
 these are always lists, though it is safe to assume that they will only include a single item. So it is safe
 to rewrite as:
-     
-    try:
-        allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes][0]
-    except IndexError:
-        pass # no gnomad exomes annotation for the variant
-           
+
+```python
+try:
+    allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes][0]
+except IndexError:
+    pass # no gnomad exomes annotation for the variant
+```
+
 #### Annotating a VCF using the client
 
 To annotate a VCF you can base your code on the VCFAnnotator object. This provides a basic implementation that
 will annotate a VCF file using a set of the available annotations. It uses [PyVCF](https://github.com/jamescasbon/PyVCF) to read and write to VCF files.
 
-    from varsome_api.vcf import VCFAnnotator
-    api_key = 'Your token'
-    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
-    vcf_file = 'input.vcf'
-    output_vcf_file = 'annotated.vcf'
-    vcf_annotator.annotate(vcf_file, output_vcf_file)
-        
+```python
+from varsome_api.vcf import VCFAnnotator
+api_key = 'Your token'
+vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
+vcf_file = 'input.vcf'
+output_vcf_file = 'annotated.vcf'
+vcf_annotator.annotate(vcf_file, output_vcf_file)
+```
+
 To annotate the VCF file with the annotations that you are interested in, you need only override 2 methods
 (`annotate_record` and `add_vcf_header_info`) in the VCFAnnotator class:
 
-    from varsome_api.vcf import VCFAnnotator
-    from vcf.parser import _Info
-    class MyVCFAnnotator(VCFAnnotator):
+```python
+from varsome_api.vcf import VCFAnnotator
+from vcf.parser import _Info
+class MyVCFAnnotator(VCFAnnotator):
+    
+    def annotate_record(self, record, variant_result):
+        """
+        :param record: vcf record object
+        :param variant_result: AnnotatedVariant object
+        :return: annotated record object
+        """
+        record.INFO['gnomad_exomes_AN'] = variant_result.gnomad_exomes_an
+        # if you wish to also include the default annotations
+        # return super().annotate_record(record, variant_result)
+        return record
     
-        def annotate_record(self, record, variant_result):
-            """
-            :param record: vcf record object
-            :param variant_result: AnnotatedVariant object
-            :return: annotated record object
-            """
-            record.INFO['gnomad_exomes_AN'] = variant_result.gnomad_exomes_an
-            # if you wish to also include the default annotations
-            # return super().annotate_record(record, variant_result)
-            return record
         
-            
-        def add_vcf_header_info(self, vcf_template):
-            """
-            Adds vcf INFO headers for the annotated values provided
-            :param vcf_template: vcf reader object
-            :return:
-            """
-            vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer',
-                                                                 'GnomAD exomes allele number value', None, None)
-            # if you wish to also include the default headers
-            # super().add_vcf_header_info(vcf_template)
+    def add_vcf_header_info(self, vcf_template):
+        """
+        Adds vcf INFO headers for the annotated values provided
+        :param vcf_template: vcf reader object
+        :return:
+        """
+        vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer',
+                                                             'GnomAD exomes allele number value', None, None)
+        # if you wish to also include the default headers
+        # super().add_vcf_header_info(vcf_template)
                                                                  
-    api_key = 'Your token'
-    vcf_annotator = MyVCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
-    vcf_file = 'input.vcf'
-    output_vcf_file = 'annotated.vcf'
-    vcf_annotator.annotate(vcf_file, output_vcf_file)
-        
+api_key = 'Your token'
+vcf_annotator = MyVCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0})
+vcf_file = 'input.vcf'
+output_vcf_file = 'annotated.vcf'
+vcf_annotator.annotate(vcf_file, output_vcf_file)
+```        
         
 ### API Documentation
 

From f8c99ceb6b29c655344d3a8323f345c37a61bf1e Mon Sep 17 00:00:00 2001
From: chapplec <charles.chapple@saphetor.com>
Date: Fri, 12 Jan 2018 15:44:23 +0100
Subject: [PATCH 21/31] changed shebang line to point to python3

---
 scripts/varsome_api_annotate_vcf.py | 2 +-
 scripts/varsome_api_run.py          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/varsome_api_annotate_vcf.py b/scripts/varsome_api_annotate_vcf.py
index 7a90db4..2ddc6c5 100755
--- a/scripts/varsome_api_annotate_vcf.py
+++ b/scripts/varsome_api_annotate_vcf.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import argparse
 import sys
 
diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py
index 5164b5d..a3b0abc 100755
--- a/scripts/varsome_api_run.py
+++ b/scripts/varsome_api_run.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import argparse
 import json
 import sys

From f7fe98a5591d5d002a3ecf757b5c40682271075f Mon Sep 17 00:00:00 2001
From: chapplec <charles.chapple@saphetor.com>
Date: Fri, 12 Jan 2018 16:07:56 +0100
Subject: [PATCH 22/31] updated python version requirement

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index dbf21a5..310721b 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 This client is still in beta but it is a good for playing around with the API.
 
 ### Python versions
-Python version 3 is supported.
+Python versions 3.5 and greater are supported.
 
 ### Installation
 We suggest that you create a python virtual environment instead of globally installing the library.

From 210761c39ab03be60bab2373d8a94097fcb47d5b Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 18:39:04 +0200
Subject: [PATCH 23/31] Changed clien to work with python v 3.3 and up

---
 setup.py              | 4 +---
 varsome_api/client.py | 6 ++++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index 95efe7a..52224b4 100755
--- a/setup.py
+++ b/setup.py
@@ -29,8 +29,6 @@
         'Intended Audience :: Science/Research',
         'Operating System :: OS Independent',
         'License :: OSI Approved :: Apache License',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.2',
         'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
@@ -42,5 +40,5 @@
         'PyVCF>=0.6.8',
         'jsonmodels>=2.2'
     ],
-    python_requires='>=3',
+    python_requires='>=3.3',
 )
diff --git a/varsome_api/client.py b/varsome_api/client.py
index 7d6c6f8..469befc 100755
--- a/varsome_api/client.py
+++ b/varsome_api/client.py
@@ -155,7 +155,8 @@ def batch_lookup(self, variants, params=None, ref_genome='hg19', max_threads=3,
         """
         results = []
 
-        async def batch(executor):
+        @asyncio.coroutine
+        def batch(executor):
             loop = asyncio.get_event_loop()
             futures = [
                 loop.run_in_executor(
@@ -166,7 +167,8 @@ async def batch(executor):
                 for queries in [variants[x:x + self.max_variants_per_batch] for x in range(0, len(variants),
                                                                                            self.max_variants_per_batch)]
             ]
-            for response in await asyncio.gather(*futures):
+            responses = yield from asyncio.gather(*futures)
+            for response in responses:
                 results.extend(response)
         # Create a limited thread pool.
         executor = concurrent.futures.ThreadPoolExecutor(

From a7b38207b6bd3d4b0e18cd848a417843f436aeab Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 18:48:27 +0200
Subject: [PATCH 24/31] Changed clien to work with python v 3.3 and up

---
 README.md |  2 +-
 setup.py  | 15 +++++++++------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 310721b..dd87353 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 This client is still in beta but it is a good for playing around with the API.
 
 ### Python versions
-Python versions 3.5 and greater are supported.
+Python versions 3.3 and greater are supported.
 
 ### Installation
 We suggest that you create a python virtual environment instead of globally installing the library.
diff --git a/setup.py b/setup.py
index 52224b4..8ecead1 100755
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,5 @@
 from setuptools import setup, find_packages
+import sys
 from os import path
 
 VERSION = (1, 0, '0b1')
@@ -6,7 +7,13 @@
 __versionstr__ = '.'.join(map(str, VERSION))
 
 here = path.abspath(path.dirname(__file__))
-
+installation_requirements = [
+    'requests>=2.0.0, <3.0.0',
+    'PyVCF>=0.6.8',
+    'jsonmodels>=2.2'
+]
+if sys.version_info < (3, 4):
+    installation_requirements.append('asyncio')
 setup(
     name='varsome_api_client',
     version=__versionstr__,
@@ -35,10 +42,6 @@
         'Programming Language :: Python :: 3.6',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
     ],
-    install_requires=[
-        'requests>=2.0.0, <3.0.0',
-        'PyVCF>=0.6.8',
-        'jsonmodels>=2.2'
-    ],
+    install_requires=installation_requirements,
     python_requires='>=3.3',
 )

From 2caef2537d221b9a2ba0e9ed646978eb1a5a5da9 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 19:26:07 +0200
Subject: [PATCH 25/31] Fixes for python 3.3, 3.4 compatibility. Supress as
 many annoying warnings in requests as possible

---
 setup.py                         |  2 +-
 varsome_api/tests/test_client.py | 18 +++++++++++++++---
 varsome_api/vcf.py               |  1 +
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/setup.py b/setup.py
index 8ecead1..c599bc5 100755
--- a/setup.py
+++ b/setup.py
@@ -13,7 +13,7 @@
     'jsonmodels>=2.2'
 ]
 if sys.version_info < (3, 4):
-    installation_requirements.append('asyncio')
+    installation_requirements.extend(['asyncio', 'unittest2'])
 setup(
     name='varsome_api_client',
     version=__versionstr__,
diff --git a/varsome_api/tests/test_client.py b/varsome_api/tests/test_client.py
index a308a72..5b59bf9 100644
--- a/varsome_api/tests/test_client.py
+++ b/varsome_api/tests/test_client.py
@@ -1,6 +1,11 @@
 import os
+
 import unittest
 from tempfile import NamedTemporaryFile
+try:
+    unittest.TestCase.subTest
+except AttributeError:
+    import unittest2 as unittest
 
 import vcf
 from vcf.parser import _Info
@@ -10,12 +15,14 @@
 
 __author__ = "ckopanos"
 
+
 API_KEY = os.getenv('VARSOME_API_KEY', None)
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 VARIANTS_CSV_FILE = os.path.join(BASE_DIR, 'tests', 'variants.csv')
 VARIANTS_VCF_FILE = os.path.join(BASE_DIR, 'tests', 'variants.vcf')
 
 
+
 class TestApiClient(unittest.TestCase):
 
     def __init__(self, methodName='runTest'):
@@ -29,12 +36,10 @@ def __init__(self, methodName='runTest'):
         else:
             self.variants_to_lookup = self.variants_to_lookup[:50]
 
-    def tearDown(self):
-        self.client.session.close()
-
     def test_schema(self):
         """Check we receive the response schema back"""
         self.assertIsNotNone(self.client.schema())
+        self.client.session.close()
 
     def test_404(self):
         """Check we can raise VarSomeAPIException"""
@@ -42,6 +47,7 @@ def test_404(self):
             self.client.lookup('chrM:410:A:T', ref_genome='hg64')
         test_exception = ve.exception
         self.assertEqual(test_exception.status, 404)
+        self.client.session.close()
 
     def test_get_lookup_hg19(self):
         """Check we can do plain get requests"""
@@ -51,6 +57,7 @@ def test_get_lookup_hg19(self):
                                                                                 'expand-pubmed-articles': 0})
                 self.assertIsNotNone(result)
                 self.assertTrue('variant_id' in result)
+                self.client.session.close()
 
     def test_batch_lookup_hg19(self):
         """Check we can do batch requests"""
@@ -58,6 +65,7 @@ def test_batch_lookup_hg19(self):
                                            params={'add-all-data': 1, 'expand-pubmed-articles': 0},
                                            raise_exceptions=True)
         self.assertEqual(len(results), len(self.variants_to_lookup))
+        self.client.session.close()
 
 
 class TestApiResponse(unittest.TestCase):
@@ -70,6 +78,7 @@ def __init__(self, methodName='runTest'):
         self.results = client.batch_lookup(self.variants_to_lookup, ref_genome='hg19',
                                            params={'add-all-data': 1, 'expand-pubmed-articles': 0},
                                            raise_exceptions=True)
+        client.session.close()
 
     def test_result_is_not_none(self):
         """Check result is not None"""
@@ -119,10 +128,13 @@ def __init__(self, methodName='runTest'):
     def test_annotate_vcf(self):
         """Check that we can annotate a vcf file"""
         output_vcf_file = NamedTemporaryFile(delete=False)
+        output_vcf_file.close()
         self.annotator.annotate(VARIANTS_VCF_FILE, output_vcf_file.name)
         vcf_reader = vcf.Reader(filename=output_vcf_file.name, strict_whitespace=True)
         self.assertTrue('gnomad_genomes_AN' in vcf_reader.infos)
         for i, record in enumerate(vcf_reader):
             with self.subTest(i=i):
                 self.assertTrue('gnomad_genomes_AN' in record.INFO)
+        vcf_reader._reader.close()
+        self.annotator.session.close()
 
diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py
index 9dbdd94..7ae4498 100755
--- a/varsome_api/vcf.py
+++ b/varsome_api/vcf.py
@@ -124,6 +124,7 @@ def annotate(self, input_vcf_file, output_vcf_file=None, template=None, **kwargs
             # we may have some variants remaining if input batch is less than batch size
         if len(input_batch) > 0:
             self._process_request(input_batch)
+        self.vcf_writer.close()
         self.logger.info("Annotating %s variants in %s. "
                          "Filtered out %s. "
                          "Errors %s" % (self.total_varialts, time.time() - annotations_start,

From c9f06e5db8b6dd8cdb11d0c22788c88b9211a9e4 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 19:36:04 +0200
Subject: [PATCH 26/31] Changed default logging handler to StreamHandler

---
 varsome_api/client.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/varsome_api/client.py b/varsome_api/client.py
index 469befc..0b53bcf 100755
--- a/varsome_api/client.py
+++ b/varsome_api/client.py
@@ -45,7 +45,7 @@ def __init__(self, api_key=None, logger=None):
             logger = logging.getLogger(__name__)
             logger.setLevel(logging.DEBUG)
             formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
-            ch = logging.FileHandler(os.path.join(BASE_DIR, 'output.log'))
+            ch = logging.StreamHandler()
             ch.setLevel(logging.DEBUG)
             ch.setFormatter(formatter)
             logger.addHandler(ch)

From 650e4cfbb80321d79774ab07f8d7b0987f55f6df Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 20:31:09 +0200
Subject: [PATCH 27/31] Changes in readme

---
 README.md          | 16 +++++++++-------
 varsome_api/vcf.py |  1 +
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index dd87353..9371c2a 100644
--- a/README.md
+++ b/README.md
@@ -5,14 +5,15 @@
 This client is still in beta but it is a good for playing around with the API.
 
 ### Python versions
-Python versions 3.3 and greater are supported.
+Requires at least Python 3.3, you can download the latest version from [www.python.org](http://www.python.org)
 
 ### Installation
 We suggest that you create a python virtual environment instead of globally installing the library.
 
 There are several ways to create a virtual environment, but you can refer to [pip installation](https://pip.pypa.io/en/stable/installing/) and
 [virtualenv installation](https://virtualenv.pypa.io/en/stable/installation/) to first install these 2 tools if you don't
-have them already installed via a package manager (Linux) or HomeBrew (MacOS), etc.
+have them already installed via a package manager (Linux) or HomeBrew (MacOS), etc. 
+Remember to use "sudo -H" when installing on Mac.
 
 To create a virtual environment, you can follow the [user guide](https://virtualenv.pypa.io/en/stable/userguide/) or simply run:
 
@@ -46,8 +47,8 @@ the client within your code instead.
     varsome_api_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1
     
 The command above will read variants from `variants.txt` and dump the annotations to `annotations.txt`. 
-If you don't use the `-k` parameter, the script will do as many requests as there are variants in `variants.txt`,
-and you will probably get an HTTP status code 429 (too many requests) error.
+For any substantial number of variants you will need to register for an API key. You can try the software without 
+the -k apiKey parameter but you will quickly get an HTTP status code 429 (too many requests) error.
 
 #### Annotating a VCF file
 To annotate a VCF file, use: 
@@ -198,12 +199,13 @@ what values the API provides as a response to lookup requests.
 
 ### How to get an API key
 
-You are generally not required to have an API key to use the API but, without one, the number of requests 
-you will be able to issue will be limited.
+To obtain an API key please [contact us](mailto:support@saphetor.com)
+
+You can use the API without an API key, but performance and the number of queries will be 
+limited in order to safeguard our platform's reliability.
 
 You will also not be able to perform batch requests without an API key.
 
-To obtain an API key please [contact us](mailto:support@saphetor.com)
 
 ### How to run the tests
 
diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py
index 7ae4498..6592408 100755
--- a/varsome_api/vcf.py
+++ b/varsome_api/vcf.py
@@ -32,6 +32,7 @@ def _process_request(self, input_batch):
                                         ref_genome=self.ref_genome, max_threads=self.max_threads)
         duration = time.time() - start
         self.logger.info('Annotated %s variants in %s' % (len(input_batch), duration))
+        self.logger.info('Writing to output vcf file')
         for i, requested_variant in enumerate(input_batch.keys()):
             try:
                 results = api_results[i]

From 79e23b77d208bc750b6096aed9053f73b4a4131a Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Fri, 12 Jan 2018 20:32:12 +0200
Subject: [PATCH 28/31] Changes in readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9371c2a..7b0ca89 100644
--- a/README.md
+++ b/README.md
@@ -199,7 +199,7 @@ what values the API provides as a response to lookup requests.
 
 ### How to get an API key
 
-To obtain an API key please [contact us](mailto:support@saphetor.com)
+To obtain an API key please [contact us](mailto:support@saphetor.com).
 
 You can use the API without an API key, but performance and the number of queries will be 
 limited in order to safeguard our platform's reliability.

From 94740931121d7cc3881032a1147d04c791fa9d35 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <ckopanos@redmob.gr>
Date: Mon, 15 Jan 2018 11:43:35 +0200
Subject: [PATCH 29/31] Update LICENSE

---
 LICENSE | 201 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 201 insertions(+)

diff --git a/LICENSE b/LICENSE
index e69de29..29f81d8 100644
--- a/LICENSE
+++ b/LICENSE
@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
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+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
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+   2. Grant of Copyright License. Subject to the terms and conditions of
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+   4. Redistribution. You may reproduce and distribute copies of the
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+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
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+          that such additional attribution notices cannot be construed
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+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
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+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
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+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

From 46a010cab552b6dd741ad5f65989d4abfa4459a8 Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Mon, 15 Jan 2018 12:53:52 +0200
Subject: [PATCH 30/31] Added license header in files

---
 scripts/varsome_api_annotate_vcf.py             | 15 +++++++++++++++
 scripts/varsome_api_run.py                      | 15 +++++++++++++++
 varsome_api/client.py                           | 14 ++++++++++++++
 varsome_api/models/elements/broad.py            | 14 ++++++++++++++
 varsome_api/models/elements/dann.py             | 14 ++++++++++++++
 varsome_api/models/elements/dbnsfp.py           | 14 ++++++++++++++
 varsome_api/models/elements/gerp.py             | 14 ++++++++++++++
 varsome_api/models/elements/gnomad.py           | 14 ++++++++++++++
 varsome_api/models/elements/gwas.py             | 14 ++++++++++++++
 varsome_api/models/elements/iarc.py             | 15 +++++++++++++++
 varsome_api/models/elements/icgc.py             | 14 ++++++++++++++
 varsome_api/models/elements/isb.py              | 14 ++++++++++++++
 varsome_api/models/elements/ncbi.py             | 14 ++++++++++++++
 varsome_api/models/elements/sanger.py           | 14 ++++++++++++++
 varsome_api/models/elements/thousand_genomes.py | 14 ++++++++++++++
 varsome_api/models/elements/transcript.py       | 15 +++++++++++++++
 varsome_api/models/elements/uniprot.py          | 15 +++++++++++++++
 varsome_api/models/elements/wustl.py            | 14 ++++++++++++++
 varsome_api/models/fields.py                    | 14 ++++++++++++++
 varsome_api/models/variant.py                   | 15 +++++++++++++++
 varsome_api/tests/test_client.py                | 15 +++++++++++++++
 varsome_api/vcf.py                              | 15 +++++++++++++++
 22 files changed, 316 insertions(+)

diff --git a/scripts/varsome_api_annotate_vcf.py b/scripts/varsome_api_annotate_vcf.py
index 2ddc6c5..b5ba68c 100755
--- a/scripts/varsome_api_annotate_vcf.py
+++ b/scripts/varsome_api_annotate_vcf.py
@@ -1,4 +1,19 @@
 #!/usr/bin/env python3
+
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import argparse
 import sys
 
diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py
index 4b4607e..3e4eb35 100755
--- a/scripts/varsome_api_run.py
+++ b/scripts/varsome_api_run.py
@@ -1,4 +1,19 @@
 #!/usr/bin/env python3
+
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import argparse
 import json
 import sys
diff --git a/varsome_api/client.py b/varsome_api/client.py
index 0b53bcf..007dfaf 100755
--- a/varsome_api/client.py
+++ b/varsome_api/client.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import logging
 import asyncio
 import concurrent.futures
diff --git a/varsome_api/models/elements/broad.py b/varsome_api/models/elements/broad.py
index 467e1ca..8642da7 100755
--- a/varsome_api/models/elements/broad.py
+++ b/varsome_api/models/elements/broad.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/dann.py b/varsome_api/models/elements/dann.py
index 6913d94..cc26d64 100755
--- a/varsome_api/models/elements/dann.py
+++ b/varsome_api/models/elements/dann.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/dbnsfp.py b/varsome_api/models/elements/dbnsfp.py
index df79a90..4dd8ef9 100755
--- a/varsome_api/models/elements/dbnsfp.py
+++ b/varsome_api/models/elements/dbnsfp.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/gerp.py b/varsome_api/models/elements/gerp.py
index 3d6b02e..56fa1f5 100755
--- a/varsome_api/models/elements/gerp.py
+++ b/varsome_api/models/elements/gerp.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/gnomad.py b/varsome_api/models/elements/gnomad.py
index 7336598..ce876f9 100755
--- a/varsome_api/models/elements/gnomad.py
+++ b/varsome_api/models/elements/gnomad.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/gwas.py b/varsome_api/models/elements/gwas.py
index 937409c..6adeaff 100755
--- a/varsome_api/models/elements/gwas.py
+++ b/varsome_api/models/elements/gwas.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/iarc.py b/varsome_api/models/elements/iarc.py
index 0263d12..89efbee 100755
--- a/varsome_api/models/elements/iarc.py
+++ b/varsome_api/models/elements/iarc.py
@@ -1,3 +1,18 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/icgc.py b/varsome_api/models/elements/icgc.py
index 903f037..ab2e752 100755
--- a/varsome_api/models/elements/icgc.py
+++ b/varsome_api/models/elements/icgc.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/isb.py b/varsome_api/models/elements/isb.py
index ae75a29..bd55e52 100755
--- a/varsome_api/models/elements/isb.py
+++ b/varsome_api/models/elements/isb.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/ncbi.py b/varsome_api/models/elements/ncbi.py
index 4703287..0b0549d 100755
--- a/varsome_api/models/elements/ncbi.py
+++ b/varsome_api/models/elements/ncbi.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 from varsome_api.models.fields import DictField
diff --git a/varsome_api/models/elements/sanger.py b/varsome_api/models/elements/sanger.py
index 18f6265..d5ee960 100755
--- a/varsome_api/models/elements/sanger.py
+++ b/varsome_api/models/elements/sanger.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/thousand_genomes.py b/varsome_api/models/elements/thousand_genomes.py
index ea9c618..62a5586 100755
--- a/varsome_api/models/elements/thousand_genomes.py
+++ b/varsome_api/models/elements/thousand_genomes.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/transcript.py b/varsome_api/models/elements/transcript.py
index 7a19918..1c0e5ad 100755
--- a/varsome_api/models/elements/transcript.py
+++ b/varsome_api/models/elements/transcript.py
@@ -1,3 +1,18 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/uniprot.py b/varsome_api/models/elements/uniprot.py
index 70b84f9..8b4d794 100755
--- a/varsome_api/models/elements/uniprot.py
+++ b/varsome_api/models/elements/uniprot.py
@@ -1,3 +1,18 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/elements/wustl.py b/varsome_api/models/elements/wustl.py
index 09aa90e..7f802db 100755
--- a/varsome_api/models/elements/wustl.py
+++ b/varsome_api/models/elements/wustl.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import models, fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/fields.py b/varsome_api/models/fields.py
index 5fc924c..c0e6a84 100755
--- a/varsome_api/models/fields.py
+++ b/varsome_api/models/fields.py
@@ -1,3 +1,17 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from jsonmodels import fields
 
 __author__ = "ckopanos"
diff --git a/varsome_api/models/variant.py b/varsome_api/models/variant.py
index 2f1f584..65aef2d 100755
--- a/varsome_api/models/variant.py
+++ b/varsome_api/models/variant.py
@@ -1,3 +1,18 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 from .fields import DictField
 from .elements import *
 
diff --git a/varsome_api/tests/test_client.py b/varsome_api/tests/test_client.py
index 5b59bf9..32e5bab 100644
--- a/varsome_api/tests/test_client.py
+++ b/varsome_api/tests/test_client.py
@@ -1,3 +1,18 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 import os
 
 import unittest
diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py
index 6592408..e4b1124 100755
--- a/varsome_api/vcf.py
+++ b/varsome_api/vcf.py
@@ -1,3 +1,18 @@
+# Copyright [2018] [Saphetor S.A.]
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 import os
 import time
 import vcf

From fee15da480518703d436f2bd3104683cedb3409d Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Mon, 15 Jan 2018 13:09:09 +0200
Subject: [PATCH 31/31] Fixed copyright message

---
 scripts/varsome_api_annotate_vcf.py             | 2 +-
 scripts/varsome_api_run.py                      | 2 +-
 varsome_api/client.py                           | 2 +-
 varsome_api/models/elements/broad.py            | 2 +-
 varsome_api/models/elements/dann.py             | 2 +-
 varsome_api/models/elements/dbnsfp.py           | 2 +-
 varsome_api/models/elements/gerp.py             | 2 +-
 varsome_api/models/elements/gnomad.py           | 2 +-
 varsome_api/models/elements/gwas.py             | 2 +-
 varsome_api/models/elements/iarc.py             | 2 +-
 varsome_api/models/elements/icgc.py             | 2 +-
 varsome_api/models/elements/isb.py              | 2 +-
 varsome_api/models/elements/ncbi.py             | 2 +-
 varsome_api/models/elements/sanger.py           | 2 +-
 varsome_api/models/elements/thousand_genomes.py | 2 +-
 varsome_api/models/elements/transcript.py       | 2 +-
 varsome_api/models/elements/uniprot.py          | 2 +-
 varsome_api/models/elements/wustl.py            | 2 +-
 varsome_api/models/fields.py                    | 2 +-
 varsome_api/models/variant.py                   | 2 +-
 varsome_api/tests/test_client.py                | 2 +-
 varsome_api/vcf.py                              | 2 +-
 22 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/scripts/varsome_api_annotate_vcf.py b/scripts/varsome_api_annotate_vcf.py
index b5ba68c..4cf5b6e 100755
--- a/scripts/varsome_api_annotate_vcf.py
+++ b/scripts/varsome_api_annotate_vcf.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py
index 3e4eb35..e8bc0da 100755
--- a/scripts/varsome_api_run.py
+++ b/scripts/varsome_api_run.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/client.py b/varsome_api/client.py
index 007dfaf..2789546 100755
--- a/varsome_api/client.py
+++ b/varsome_api/client.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/broad.py b/varsome_api/models/elements/broad.py
index 8642da7..6c994f9 100755
--- a/varsome_api/models/elements/broad.py
+++ b/varsome_api/models/elements/broad.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/dann.py b/varsome_api/models/elements/dann.py
index cc26d64..30d7a73 100755
--- a/varsome_api/models/elements/dann.py
+++ b/varsome_api/models/elements/dann.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/dbnsfp.py b/varsome_api/models/elements/dbnsfp.py
index 4dd8ef9..b652327 100755
--- a/varsome_api/models/elements/dbnsfp.py
+++ b/varsome_api/models/elements/dbnsfp.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/gerp.py b/varsome_api/models/elements/gerp.py
index 56fa1f5..06b34b3 100755
--- a/varsome_api/models/elements/gerp.py
+++ b/varsome_api/models/elements/gerp.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/gnomad.py b/varsome_api/models/elements/gnomad.py
index ce876f9..4baf52d 100755
--- a/varsome_api/models/elements/gnomad.py
+++ b/varsome_api/models/elements/gnomad.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/gwas.py b/varsome_api/models/elements/gwas.py
index 6adeaff..f339728 100755
--- a/varsome_api/models/elements/gwas.py
+++ b/varsome_api/models/elements/gwas.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/iarc.py b/varsome_api/models/elements/iarc.py
index 89efbee..a3db37f 100755
--- a/varsome_api/models/elements/iarc.py
+++ b/varsome_api/models/elements/iarc.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/icgc.py b/varsome_api/models/elements/icgc.py
index ab2e752..8cfbaa0 100755
--- a/varsome_api/models/elements/icgc.py
+++ b/varsome_api/models/elements/icgc.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/isb.py b/varsome_api/models/elements/isb.py
index bd55e52..33897c8 100755
--- a/varsome_api/models/elements/isb.py
+++ b/varsome_api/models/elements/isb.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/ncbi.py b/varsome_api/models/elements/ncbi.py
index 0b0549d..7b758f8 100755
--- a/varsome_api/models/elements/ncbi.py
+++ b/varsome_api/models/elements/ncbi.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/sanger.py b/varsome_api/models/elements/sanger.py
index d5ee960..de8a12f 100755
--- a/varsome_api/models/elements/sanger.py
+++ b/varsome_api/models/elements/sanger.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/thousand_genomes.py b/varsome_api/models/elements/thousand_genomes.py
index 62a5586..20e79cf 100755
--- a/varsome_api/models/elements/thousand_genomes.py
+++ b/varsome_api/models/elements/thousand_genomes.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/transcript.py b/varsome_api/models/elements/transcript.py
index 1c0e5ad..0b9b2af 100755
--- a/varsome_api/models/elements/transcript.py
+++ b/varsome_api/models/elements/transcript.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/uniprot.py b/varsome_api/models/elements/uniprot.py
index 8b4d794..30855da 100755
--- a/varsome_api/models/elements/uniprot.py
+++ b/varsome_api/models/elements/uniprot.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/elements/wustl.py b/varsome_api/models/elements/wustl.py
index 7f802db..e2633d7 100755
--- a/varsome_api/models/elements/wustl.py
+++ b/varsome_api/models/elements/wustl.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/fields.py b/varsome_api/models/fields.py
index c0e6a84..a3e8f23 100755
--- a/varsome_api/models/fields.py
+++ b/varsome_api/models/fields.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/models/variant.py b/varsome_api/models/variant.py
index 65aef2d..bdc19a2 100755
--- a/varsome_api/models/variant.py
+++ b/varsome_api/models/variant.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/tests/test_client.py b/varsome_api/tests/test_client.py
index 32e5bab..8f736f4 100644
--- a/varsome_api/tests/test_client.py
+++ b/varsome_api/tests/test_client.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py
index e4b1124..752e726 100755
--- a/varsome_api/vcf.py
+++ b/varsome_api/vcf.py
@@ -1,4 +1,4 @@
-# Copyright [2018] [Saphetor S.A.]
+# Copyright 2018 Saphetor S.A.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.