gatk3-germline-snps-indels

GATK3 and this workflow is now longer supported, this repo is intended for legacy purposes.

Purpose :

Workflow for germline short variant discovery with GATK3.

haplotypecaller-vcf-gatk :

The haplotypecaller-vcf-gatk3 workflow runs HaplotypeCaller from GATK3 in VCF mode on a single sample according to the GATK Best Practices (June 2016), scattered across intervals.

Requirements/expectations

• One analysis-ready BAM file for a single sample (as identified in RG:SM)
• Set of variant calling intervals lists for the scatter, provided in a file

Outputs

• One VCF file and its index

Software version requirements :

• GATK 3
• Samtools (see gotc docker)
• Python 2.7

Cromwell version support

• Successfully tested on v33
• Does not work on versions < v23 due to output syntax

IMPORTANT NOTE :

• Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
• This repo only contains the HaplotypeCaller workflow which produces a VCF, a GVCF workflow has not been made available. The availability of GVCF workflow will depend on whether or not there is strong user interest, let us know on the gatk forum.
• The HaplotypeCaller workflow can produce GVCF by setting the make_gvcf variable to true.