Picard AddOrReplaceReadGroups,

Question

[María José]

Hi,

I am using Picard's AddOrReplaceReadGroups and I would like to ask the appropiate values for each field. or could I assign any names I choose?. I have fastq files and I don't know if reads identifiers contain any information that need to be included in the different fields of RGID, RGSM, RGPU, or RGPL.

Answer 1

[Pierre Lindenbaum]

see "Meaning of the read group fields required by GATK"

https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups