Adding Coverage Stats into MuTect2 output VCFs

Question

[John Ma]

MuTect2's output only includes AD parameters, but for our QC pipeline we would like DP(4) data to ensure uniformity across different variation callers. While there are certain other ways I can obtain these kind of data and use that in a multi-file analyses, is there a way I can add read counts into the MuTect2 output such that it can be filtered using standard VCF parsers? Thanks for the help!

Answer 1

[gil.hornung]

I came across this as well. Why remove the DP data from the VCF?