Using GATK AddOrReplaceReadGroups

Question

[vctrm67]

Quick question regarding using AddOrReplaceReadGroups: if I have a BAM file that correspond to a single sample, but is comprised of multiple lanes, is it appropriate to use AddOrReplaceReadGroups to replace all read groups with a single read group for ease of downstream analysis? To my understanding, since all the lanes correspond to the same sample, the read groups should be the same if I don't care about the lanes themselves.

Answer 1

[Pierre Lindenbaum]

is it appropriate to use AddOrReplaceReadGroups to replace all read groups with a single read group for ease of downstream analysis?

it shouldn't break your workflow, but you might miss an opportunity to run a quality control per lane.