Hi, I have made a PON from my normal samples and want to combine this with the PON from GATK. Is this possible? Or any other way of using both when running mutect2?
REQUIRED for all errors and issues: a) GATK version used: 126.96.36.199 I am running mutect2 in tumor-normal mode which gives ONE output file. I am puzzled by which inputs I should use for CalculateCon...