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.
So looking back at a previous analysis, I noticed that BaseRecalibrator took about 16 hours, but then PrintReads took another 48, which seems egregious.
My plan is to run PrintReads separately on different loci, each using the "merged" table from BaseRecalibrator, and then merge the resulting BAM files.
I'd be surprised if this isn't equivalent to running PrintReads on the whole genome at once, but I just wanted to check with the experts here.