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.

GATK Unified Genotyper multiple-sample

liujieliujie GermanyMember

When I use Unified Genotyper with multiple-sample, the samples should be of the same kind ? Can I put the cancer samples and normal samples together ?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @liujie,

    You should not be calling variants on cancer samples with the GATK callers, because they are not designed to deal with cancer-specific error models. You should use MuTect instead. If you have paired tumor and normal samples, MuTect will be able to process them together intelligently.

Sign In or Register to comment.