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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Alternative resources for Mutect2/GetPileupSummaries when dealing with genome data


I'm currently using GATK, following the best practices for somatic variant calling. I already have this set up for exomes, but I'm now attempting to run the same pipeline on genome data.

I'm using the gnomAD "af-only-gnomad.raw.sites.b37.vcf" file as the germline resource for Mutect2, and I'm using the "small_exac_common_3_b37.vcf.gz" file (both from the bundle) as the -V and -L arguments for GetPileupSummaries when running exomes - are these the correct resources for genomes as well? Or is there another resource you recommend?




  • akovalskakovalsk Member, Broadie, Moderator admin

    Hi @michaelmc thanks for your question.

    Those should be appropriate, but in general we recommend carefully considering the intervals (or the subsetting of the variant file) as we expect off-target reads to be poorly or even erroneously covered.

  • michaelmcmichaelmc Member
    Thanks for the answer - I was asking mainly because it was recommended to use the same file (in most cases) for both -V and -L options in GetPileupSummaries in this thread:


    Is the ExAC resource suitable for genomes in this case? Or would gnomAD or another resource that incorporates whole genome data be appropriate?
  • akovalskakovalsk Member, Broadie, Moderator admin

    Hi @michaelmc yes that resource is suitable.

Sign In or Register to comment.