Question: GATK Mutect2 tumor-segmentation table
1
gravatar for cocchi.e89
10 weeks ago by
cocchi.e89110
cocchi.e89110 wrote:

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!

somatic mutect2 gatk • 151 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by cocchi.e89110
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