It looks like you're new here. If you want to get involved, click one of these buttons!
I'm running the UnifiedGenotyper (gatk version 2.0-35) with -glm INDEL on a dataset.
When I use -glm SNP everything works fine and I get my SNV calls, but if I use INDEL I get the following Error message:
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (149) > (100) STOP -- this should never happen -- call Mauricio!
It looks like something is up with the read coordinates. I ran this particular script with -L 1 to limit to chromosome 1 but when I check the first and last reads of this chromosome everything seems to be in order (at least they map within the chromosome coordinates).