error converting VCF to varmap

[fac2003]

Got this error on a VCF file. At the very least the error should show the line position causing the error. At the moment it is impossible to diagnose the source of the problem.
Exception in thread "main" java.lang.InternalError: indel must either be an insertionInRead or a deletion
at org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator.insertionInRead(EquivalentIndelRegionCalculator.java:279)
at org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator.determine(EquivalentIndelRegionCalculator.java:152)
at org.campagnelab.goby.util.VariantMapCreator.realign(VariantMapCreator.java:121)
at org.campagnelab.goby.util.VariantMapCreator.addVariant(VariantMapCreator.java:55)
at org.campagnelab.goby.modes.VCFToGenotypeMapMode.execute(VCFToGenotypeMapMode.java:226)
at org.campagnelab.goby.modes.GenericToolsDriver.execute(GenericToolsDriver.java:214)
at org.campagnelab.goby.modes.GobyDriver.main(GobyDriver.java:56)