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, VQSLOD, and indels
Hi Mark, Eric -
First, I wanted to thank you guys for providing advice with respect to running VQSR. I am already sold and a huge fan of the method :-).
I was wondering if either of you could comment on VQSLOD and sensitivity filter tranche?
To be more specific, if I set a filter threshold of 99% for sensitivity and VQSLOD < 0 I imagine that probably is not a good idea! However, a VQSLOD of 3 or 5 may be appropriate in the statistical sense, i.e. pretty confident that this is a real variant. Finally, I am thinking we should include VQSLOD in our statistical genetic association mapping methods. I wanted to get a sense from either of you what VQSLOD you would want to completely remove from analysis?