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.
Quality for Invariant Sites?
I have been successfully using the GATK pipeline and Unified Genotyper to call snps. However, I really need GQ scores for invariant sites as well as variant sites.
Currently at invariant sites, only GT and DP are outputted. Is it possible to also get GQ for these sites? I can't seem to find how to do this.