Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.
Hi GATK team,
I have 2 tumor samples and 1 normal sample, all for the same patient. How can I do with the estimation of contamination (GetPileupSummaries,CalculateContamination) ? Is yet possible to calculate it with two tumor samples and use it at the end in the "FilterMutectCalls" step?
If yes, I have to run 3 GetPileupSummaries commands (tumor1, tumor2, normal) and then use two tumor input files (pileup summaries tables; tumor 1 and tumor 2 ) in the CalculateContamination step?
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