TRTools

TRTools includes a variety of utilities for filtering, quality control and analysis of short tandem repeats (STRs) and variable number tandem repeats (VNTRs) downstream of genotyping them from next-generation sequencing. It supports multiple recent genotyping tools (see below).

See full documentation and examples at https://trtools.readthedocs.io/en/latest/.

Install

You can obtain TRTools from pip:

pip install trtools

Or, to install from source, run the following command from the base directory of the TRTools repo:

python setup.py install [--prefix=PREFIX]

to install locally, set --prefix=$HOME and ensure $HOME is on your PYTHONPATH.

(Note, required package pybedtools requires zlib. If you receive an error about a missing file zlib.h, you can install on Ubuntu using sudo apt-get install zlib1g-dev or CentOS using sudo yum install zlib-devel.)

Tools

TRTools includes the following tools.

• dumpSTR: a tool for filtering VCF files with STR/VNTR genotypes
• mergeSTR: a tool to merge VCF files across multiple samples genotyped using the same tool
• statSTR: a tool for computing various statistics on VCF files
• compareSTR: a tool for comparing TR callsets
• qcSTR: a tool for generating various quality control plots for a TR callset

Type <command> --help to see a full set of options.

It additionally includes a python library, trtools, which can be accessed from within Python scripts. e.g.:

import trtools.utils.utils as stls
allele_freqs = {5: 0.5, 6: 0.5} # 50% of alleles have 5 repeat copies, 50% have 6
stls.GetHeterozygosity(allele_freqs) # should return 0.5

Usage

See the README in each subdirectory for usage details.

Supported Tools

TRTools supports VCFs from the following STR/VNTR genotyping tools:

• GangSTR version 2.4 or higher.
• HipSTR
• PopSTR
• ExpansionHunter
• AdVNTR

Contributing

If you would like to contribute a fix or new tool to TRTools, follow these guidelines:

• Fork the repository.
• Make your changes.
• Ensure all functions, modules, classes etc. conform to Numpy docstring standards (https://numpydoc.readthedocs.io/en/latest/format.html).
• Add tests (see tests/ folder to find the appropriate location for new tests) to test any new functionality. To make sure pytest knows about them, you may need to edit pytest.ini.
• Run pytest --cov=. --cov-report term-missing to make sure that (1) all tests pass and (2) any code you have added is covered by tests.
• If applicable, update REAMDEs with new usage information.
• Submit a pull request, with a reasonably descriptive message of what changes you have made.