Advice on troubleshooting 'ERROR MESSAGE: Badly formed genome loc'
Hi I am getting the following error message using IndelRealigner in GATK 2.8.1
ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 114033418 is less than start 114033419 in contig 13
I checked the targetIntervals file for these coordinates and I see
which seems fine. Other samples which were processed using the exact same steps look ok. I checked the bam files and there are only a few reads overlapping this site. But this is an off capture site so I see the same thing in other samples as well. Any advice would be most helpful. Thank you.