Tool version: GATK220.127.116.11
Sample: Whole genome sequence, human cancer.
I need "allelic depth" (i.e, DepthPerAlleleBySample in Haplotypecaller)information in somatic.vcf for some further analysis. I am using Mutect2 for somatic SVN calling according to current best practice for somatic SNV calling in GATK.
Haplotypecaller has function to calculate "allelic depth", but Mutect2 does not.
How do I add allelic depth to Mutect2 output vcf files? Does anyone have suggestion?
Please sign in to leave a comment.