diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index aea63b61d..14d647b6d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -361,6 +361,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         final int hsize = (int)ref.getWindow().size()-Math.abs(eventLength)-1;
         final int numPrefBases= ref.getLocus().getStart()-ref.getWindow().getStart()+1;
 
+        if (hsize <=0) {
+            logger.warn(String.format("Warning: event at location %s can't be genotyped, skipping",loc.toString()));
+            return null;
+        }
         haplotypeMap = Haplotype.makeHaplotypeListFromAlleles(alleleList, loc.getStart(),
                 ref, hsize, numPrefBases);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 8d9768681..a06a7166f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -285,7 +285,7 @@ public class GenomeLocParser {
             return vglHelper(exceptOnError, String.format("Unknown contig %s", contig));
 
         if (stop < start)
-            return vglHelper(exceptOnError, String.format("The stop position %d is less than start %d", stop, start));
+            return vglHelper(exceptOnError, String.format("The stop position %d is less than start %d in contig %s", stop, start, contig));
 
         if (contigIndex < 0)
             return vglHelper(exceptOnError, String.format("The contig index %d is less than 0", contigIndex));