Whole Genome Sequencing Structural Variation Pipeline

Quick start

Install nextflow

curl -fsSL get.nextflow.io | bash
mv ./nextflow ~/bin

Run the pipeline

nextflow run NBISweden/wgs-structvar --project <uppmax_project_id> --bam <bamfile.bam> --run_all

This will run both manta and fermikit and create summary files for everything in the results subdirectory.

It is recommended that you set the environment variable NXF_WORK to something like

export NXF_WORK=$SNIC_NOBACKUP/work

Preferably in your .bashrc.

General information

This is a pipeline for running the two structural variation callers fermikit and manta on UPPMAX.

You can choose to run either of the two structural variation callers or both (and generate summary files).

Masking

The pipeline will use the following mask files to remove known artifacts:

• From cc2qe/speedseq: https://github.com/cc2qe/speedseq/raw/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
• From lh3/varcmp: https://github.com/lh3/varcmp/raw/master/scripts/LCR-hs37d5.bed.gz

External links

• NextFlow website
• NextFlow gitter chat