Entering edit mode
4.3 years ago
cocchi.e89
▴
290
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
and this -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!