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.
Recommended/required sequencing depth for standard diploid, whole-genome, germline variant calling
I was searching the GATK best practices for a recommended or required sequencing depth for standard whole-genome germline variant calling on a diploid species (humans, specifically). I know general word of mouth is at least 30x, but can you clarify GATK's recommendations or requirements?
1. I know this is not super easy to determine, but what is the approximate required depth for UnifiedGenotyped (GATK v3.X)? How about recommended?
2. Similarly, what are the required and recommended depths for HaplotypeCaller?
I'm trying to determine the approximate coverage at which you would not trust a specific variant. I realize this is very context specific, but a general recommendation would be super helpful.