I am currently processing my .bam files using Picard and GATK. However, I have come across the missing read group error, and realised that I have either lost, or never assigned read group information when using BWA to map my reads to the reference. I have already merged by .bam files for each individual in my study.
My question is whether it's appropriate to use Picard's AddOrReplaceReadGroups function to add read groups to merged bams? Typically, each individual is made up of read from around 6 different lanes, and it appears that this data was generated using several different sequencing platforms.
Please let me know if more information is necessary to determine whether or not my position is salvageable.
Thanks for your time.