Read group header line

Question

[win]

Hi all,

I have a pair of FASTQ files which I aligned using BowTie2 and tried to run GATK on the resulting BAM. GATK complained that the RG header is missing. According to this post Picard tools can actually add the RG lines but I do not know what values to supply for RG line header.

Similarly in BowTie2 also there is an option to specify if RG line header but again not sure what values can be added there?

Can someone please help with this as to what values to add when all we have is the FASTQ files.

Thanks in advance.

Answer 1

[Devon Ryan]

If you're only calling variants in a single file it doesn't matter what the read group information is. You can just use "foo" or "value" or "iamareadgroup" or anything else. Read groups are useful for grouping alignments by samples across files, or library preparations within samples, or sequencing platforms across samples (e.g., for bias correction), and things like that.

[Domu]

Hey, what if I want to call variants using the cohort calling option of GATK? Does it matter then?