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.
Is there a way to limit the genotyping to those sites with FILTER=PASS?
With the genotyping discovery qscript, all the discovery sites were genotyped during the run instead of the much smaller set that have filter=PASS.
Instead of having all these sites genotyped, is there a option to specify that only sites with filter=PASS should be genotyped and output to the final vcf file. Or is there a reason these non PASS sites are included?