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:
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?