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!

Germline CNV, ploidy and best practices


I'm looking to test the germline CNV tool but I'm having trouble understanding what is the --contig-ploidy-priors file that is needed for DetermineGermlineContigPloidy. Is there a reference I can download or do I have to generate the file somehow? (I'm working on WES samples)
Also, when can we expect the best practices workflow for Germline CNV? It could hold the answer I need.

Many thanks,

Best Answer


  • kimykimy Member
    Ok thank you!
    So this is a default file that can be adjusted, right?
    And I'm guessing that CollectFragmentCounts was renamed CollectReadCounts in the version?
  • AdelaideRAdelaideR Member admin

    Yes, we are about to release a better description of the workflow to follow, so keep your eyes on the board. Thank you for pointing out the name change.

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