REQUIRED for all errors and issues:
a) GATK version used: 188.8.131.52
I am running mutect2 in tumor-normal mode which gives ONE output file. I am puzzled by which inputs I should use for CalculateContamination. My input for GetPileupSummaries is the ONE file that are output from Mutect2. So, which file should be provided for the --matched-normal parameter? Since I have not run GetPileupSummaries on the normal samples.
Please sign in to leave a comment.