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.
Notice:
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.
Attention:
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!

MuTect 2 - coverage depth of somatic, germline, and PoN data

robcrobc irelandMember
edited July 22 in Ask the GATK team
I have a question about MuTect 2 and using data sources at different depths of coverage.

My somatic source is targeted gene panel sequenced to an average of 500x, my germline source is the same targeted panel but sequenced to an average of 100x, and my PoN is 100 individuals whole exome sequenced to an average of 60x.

Is there a risk of skewing the weight of the statistical variant calling model and / or batch effects with the above setup? I'm particulalry concerned with the five-fold difference between the germline and somatic data - or is 100x deep enough for Mutect to be confident with the germline calls?
Tagged:

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    edited July 23

    Spoke with the dev team:

    your setup is fine, there should be no issue due to the differing coverages. 100x is quite deep enough for confident germline calling which will be used for filtering with the normal.

Sign In or Register to comment.