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Test-drive the GATK tools and Best Practices pipelines on Terra
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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.