Gatk germline short variant discovery

GATK: Germline Short Variant Discovery

Official Documentation:

The Germline Variant Discovery workflow runs the GATK4 HaplotypeCaller tool in GVCF mode on a single sample according to GATK Best Practices. When executed the workflow scatters the HaplotypeCaller tool over the input bam sample using an interval list file. The output produced by the workflow will be a single GVCF file which can then be provided to GenomicsDBImport along with several other GVCF files to call for variants simultaneously, producing a multisample VCF.

Workflow Repository: github.com/gatk-workflows/gatk4-germline-snps-indels