If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Weird VQSR filtering pattern
I performed HC joint calling against 300 normal tissue samples. I did every step according to the best practice and got a VQSR plot very similar to this one. Most variants have the same MQ and FS value and make these feature distribution non-gaussian. Would such result be still valid? Can anyone share some insight?