Missing read group in BAM files

Question

[Begonia_pavonina]

Hello everyone,

I have processed PE reads through the pipeline HybPiper to align them to a reference genome with GATK.

But inspecting the output BAM files with the GATK tool ValidateSamFile, I found out a very common error in the error report:

WARNING::RECORD_MISSING_READ_GROUP

The problem has been discussed in the thread below, but the reason of this error is never explained in details, or controversial (quality cutoff too high?)

Has anyone had the same issue? What could be the origin of the problem?

How to fix .bam file that was diagnosed as "MISSING_READ_GROUP" by Picard ValidateSamFile

Answer 1

[swbarnes2]

Pierre's answer from your link is right.