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.
Apply VQSR to variants called by other tools
Hi, I have several variant files that were generated by other calling tools with some annotations not defined by GATK. I wonder if I can also apply VQSR on these dataset restricting to those exclusive annotations (using "-an"). Is there any drawback for this application?
Besides, I saw somewhere that fitting only a single Gaussian distribution to each annotation. Is this a proper way to perform variant recalibration?