Can you please provide
a) GATK version used gatk-184.108.40.206
b) Exact GATK commands used gatk CalculateContamination -I getpileupsummaries.table -O calculatecontamination.table -tumor-segmentation segments.table
c) The entire error log if applicable.
Dear GATK team,
I was under impression you need to process each tumor and generate 1) segments and 2) calculate contamination tables.
Now how do you feed them to FilterMutectCalls if you have multiple tumor samples? I was not able to locate the tutorial describing this.
gatk FilterMutectCalls -V unfiltered.vcf \ [--tumor-segmentation segments.table] \ [--contamination-table contamination.table] \ --ob-priors read-orientation-model.tar.gz \ -O filtered.vcf
I would greatly appreciate it if GATK dev members (or anyone else who encountered this before) could guide me how to proceed.
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