UnifiedGenotyper glm mode INDEL error
Posted in Ask the GATK team | Last updated on 2012-10-18 00:51:39

Comments (9)


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).

Cheers, Paul

Return to top Comment on this article in the forum