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How is "germline_risk" failure reason for MuTect assigned?

nsticklenstickle TorontoMember

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!
Natalie

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?

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @nstickle
    Hi Natalie,

    I moved your question to the MuTect category. Someone will help with this soon.

    I am going to delete your other post.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Some of this is described in the Cibulskis et al paper describing MuTect. Whatever is not in there is not currently documented, and we are now focusing our efforts on documenting Mutect2, so we will not be able to provide more support for MuTect.

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