Could you clarify something for my own understanding please?
I have read your post https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups on read groups and understand what they are.
My question is, if I have the same library run on the same flowcell over multiple lanes, do I need to preserve this lane information for downstream applications such as Mark (optical) duplicates?
Therefore would it be incorrect to concatenate the fastqs from different lanes before assigning read group information at the alignment stage?
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