[GATK] [MuTect2] [RNA-Seq] Adding read group ahead of annotations

Question

[umn_bist]

If I am working with a large set of paired end RNA-seq samples (matched tumor, normal). In which part of the pipeline is the RG suppose to be naturally added into the header for RNA-Seq. I saw Bowtie2 has an option but I am wondering if it's common to align RNA-seq in a splice-nonaware aligner before TopHat for the sole purpose of retrieving a bam file with RG in its header.

Ideally, picard AddOrReplaceReadGroup will work but I cannot individually fetch and input the appropriate tag value for RG-ID for each paired-end samples. Thank you very much for your time and help.

Answer 1

[Patrick_Reed]

I think the optimal time to add a RG tag is either during alignment (if possible) or post-alignment before any further processing. Can you elaborate on why you cannot call picard on each aligned sample?