How is "germline_risk" failure reason for MuTect assigned?
Can you provide some more information about how the "germline_risk" failure reason is assigned in MuTect?
As an example:
a site in dbsnp with normal_f =0 and tumor_f=0.28 and tumor_power=0.612407
It is the tumor_power data combined with this variant being present in dbsnp that results in the failure reason "germline_risk"? And how is the tumor_power determined?
Thanks for your help!
I posted this as a comment on this page, but am unsure if it gets seen that way, so re-entering it now as a question - sorry if this is a repeat: http://gatkforums.broadinstitute.org/gatk/discussion/6896/germline-risk-variant-calling-for-cancer-wes?