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.
Why are measured base insertion and deletion qualities only Q45 for BaseRecalibrator?
The measured qualities of the BI and BD are 45 in for this library. Normally I have a wide range for I and D qualities from 39-61. I have tried setting -ddq and -idq to -1, but that doesn't change anything. I am using dbsnp137 for my knowns, and otherwise just use default settings.