Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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!

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?



  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Natalie,

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

    I am going to delete your other post.


  • 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.

Sign In or Register to comment.