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.
How to edit MULTIPLE read groups in one bam file
I recently received a WGS bam from Broad for 1 sample, but with about 8 read groups. BSQR kicked it back saying that the sequencer name in the read group is not recognized.
Anyways, I need to edit the sequencer name so that BSQR can run. AddReplaceReadGroups in Picard will toss out the 8 RGs and add 1 RG info, so that will not work. So how do you edit one or two of the RGs, or replace all 8 RGs in the bam?
I am sure this is a common issue.