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.
Can ApplyBQSR emit queryname sorted BAM?
I am using GATK v 4.1.2. I would like to produce queryname sorted BAM output from ApplyBQSR. The input BAM for the BaseRecalibrator step is queryname sorted. Is there a way to instruct the tool to output a specific sort order? I would very much like to avoid an additional sort step, and queryname sorting is required by the next tool in my pipeline (SAMblaster).
Thanks in advance,