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.

Build a panel of normal for Mutect

steste auMember


I am trying to build a panel of normal for Mutect. After a deep investigation on internet I could not find anything more specific that this:

"ran MuTect on a set of normal samples as if they were tumor samples without a matched normal sample in STD mode. From these data, a VCF file is created for the sites that were identified as variant by MuTect in more than one normal sample." (from

The sentence "From these data, a VCF file is created" is not self explanatory.

Could someone please indicate clearly the command line(s) needed for this procedure? Including (for example) 4 normal samples.

This think this will be extremely useful for the whole community.

Thanks a lot,

Bioinformatician at The University of Melbourne
Royal Melbourne Hospital


  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Hi Stefano,

    When you run MuTect on the normal samples that you want to include in your panel of normals, one of the outputs is a VCF file. That's what "a VCF file is created" means; no additional processing is needed. Does that clarify things?

  • steste auMember

    Thanks Geraldine,

    yes partially. Your answer makes me understand that I have to feed Mutect with multiple files to obtain one VCF file (rather than integrate multiple VCF files afterwards).

    Now the question is (which I looked for, already): can you write an example command line to execute Mutect with multiple **normal ** files?

    Browsing around, I realized how this would be useful for the community.

    Thanks a lot,

  • steste auMember

    Or, should I **merge ** the BAM files before submission?

  • steste auMember

    Thanks Geraldine,

    much appreciated.


Sign In or Register to comment.