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.
VQSR Resources for Indels
I noticed that on the page for setting the right arguments for VQSR you mentioned that Mills and dbSNP should be used as resources for INDEL variant recalibration. However, at the bottom of the page, it is said that the apply recalibration step for INDELs should use Mills and 1000G. Since these two tools are used together, I would like to know which combination of resource files to pass on to them: Mills/dbSNP or Mills/1000G.