Indel Realigner - Exception counting mismatches AND Missing read group or read group not defined
For the past several months, I have consistently been receiving 2 error messages depending on which version of GATK I am using.
If I use an older version (such as 1.0.5588), I am able to successfully generate the intervals file using RealignerTargetCreator with no problems. When I then run IndelRealigner, I receive messages for individual reads about Exception counting mismatches. I typically remove these reads by hand (even though there appears to be nothing wrong with them) and carry on. When I then move to the UnifiedGenotyper to call SNPs, I use the realigned output file from the IndelRealigner and now get the message about missing read group or read group not defined. However, the input bam file for the IndelRealigner worked just fine. But the output from the IndelRealigner now has a read group issue. I don't understand
If I use a newer version (2.3.9 or 2.4.9), I immediately get the message about missing read group or read group not defined when I first run RealignerTargetCreator. When I look at the headers from the bam file, everything seems correct.
I have double checked my reference file, its index, my bam file and the index bam file. Nothing seems to have an error.
Any suggestions on how to move forward? I have been troubleshooting for months with other colleagues and have gotten nowhere. Thank you for your time and recommendations.