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.

ReadBackedPhasing of somatic and germline variants?

RightOnTimeRightOnTime AmsterdamMember
edited February 2018 in Ask the GATK team

Hi all,

I'd like to know which germline variants are proximal to and on the same chromosome as detected somatic variants. Is there an out-of-the-box way to phase germline and somatic variants to one another? If not, do you see a role for GATK ReadBackedPhasing?

Thanks for your help and my apologies if this has been answered already, I couldn't find anything related.



  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi M,

    There is currently no easy way to do this. Mutect2 only outputs the somatic sites. However, there are plans to have Mutect2 output both somatic and germline variants. That should be coming soonish.


Sign In or Register to comment.