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.
changing MAPQs in aligned bam files
I use a pipeline of Picard's MarkDuplicates, RealignTargetCreator, IndelRealigner, BaseRecalibrator, PrintReads. I noticed a small but consistent increase in reads with MAPQ >= 20 from the initial bam file to the final bam file. Any idea where this could be happening? I didn't think any of those tools changed MAPQ, but I'm assuming I'm wrong.