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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! at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:512) [...]
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).