Adding Coverage Stats into MuTect2 output VCFs
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!
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I came across this as well. Why remove the DP data from the VCF?
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