Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.