I am working on somatic calling using GATK Mutect2 and following their best practice guidelines they now have a CalculateContamination step whose example states:
gatk CalculateContamination \ -I getpileupsummaries.table \ -tumor-segmentation segments.table \ -O calculatecontamination.table
-tumor-segmentation segments.table was never mentioned before nor is specified how to generate such file.
I think it might be the
.modelFinal.seg file with CNV/SV segments that you can generate through ModelSegments but I was wondering what is the role of such file in this somatic calling pipeline...is it for filtering out possible somatic variants that are found in CNV/SV regions?
Thank you very much in advance for any help!