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.
BQSR: using COSMIC for knownSites?
I am planning to run MuTect2 on some tumor sample pairs. Of course I will put all the bundle files as BQSR's knownSites, but I wonder if it is a good idea to also put the current COSMIC variations as knownSites as well? Since the samples are cancer cells/tissue, it may be a good idea to avoid known cancer-causing variations from being seen as sequencing errors, but then I also fear it would cause too much false positives...