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.

Mutect2 outputting samples with AD of "."

I've setup a workflow that runs Mutect2, which completes successfully, but the AD of all variants is output as "."

This is an issue as we use the AD for downstream stages. Is there any reason this might be happening?

I have attached both the VCF that is missing the AD field, and the log from our workflow that includes the GATK logging. Everything there seems fine, but perhaps I'm missing something.


Sign In or Register to comment.