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.
Does MuTect 1.1.4 properly handle reads aligned with bwa mem, with or without '-M'?
I have BAMs aligned with bwa mem and the '-M' flag was not used, so supplementary read alignments are not marked as secondary. I am wondering if MuTect v1.1.4 will ignore these reads or if I should realign with bwa mem -M to mark these alignments as secondary.