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 does GATK4 Mutect2 know which -I is tumor?


I'm reading the Mutect2 documentation here:


I see that you give two -I arguments. How does Mutect2 know which is the tumor? Is it whichever comes first, or is it related to the placement of the -tumor argument?


Best Answer


  • Nevermind, I think I understand. It's actually using the SM tag on the reads, right? So I could even put the tumor and normal in one BAM file, and just have one -I argument, and it will sort them out by looking for SM tags matching the -tumor and -normal arguments I gave.

Sign In or Register to comment.