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.
Depth of coverage in GATK 4
I'm trying to find the depth of coverage for a targeted sequencing project using GATK 4, but I'm confused about which tool I can do this with. I've combed over the list of new tools and have tried the CollectHsMetrics and CollectFragmentCounts tools. Are these the "new" DepthOfCoverage tool of GATK 3.8? What is everyone else using for DepthOfCoverage using GATK 4? Any guidance or tips would be appreciated. Thank you!