This workflow represents the GATK Best Practices for SNP and INDEL calling on DNA data.
Starting from a processed BAM file, the workflow performs variant calling with respect to the reference genome. Depending on HaplotypeCaller’s output file type (VCF or g.VCF, the resulting file of this workflow can be used as a stand alone result for single-sample analysis, or as one of the cohort files downstream joint calling analysis. On the GATK website you can find more detailed informat
This is a companion discussion topic for the original entry at github.com/sevenbridges-openworkflows/Broad-Best-Practice-Germline-snps-and-indels-variant-calling-CWL1.0-workflow-GATK-188.8.131.52