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.
Regarding MuTect default Mapping Quality filters
I was wondering what is the default Mapping Quality cutoff for Mutect, Since when I get coverage for any given position, with other tools, I get a much deeper coverage than what MuTect registers. I would like to apply the same cutoff to the other tool so the two outputs are compatible.