Workflow for germline short variant discovery with GATK3.
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.
- 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
- One VCF file and its index
- 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
- 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 totrue
.