The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?