diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 3ea1bb5d6..1712f6f7b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -440,7 +440,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @return vc subcontext
      */
     public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Set<Allele> alleles) {
-        return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), filtersWereApplied() ? getFilters() : null, getAttributes());
+        return new VariantContext(getSource(), contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, getNegLog10PError(), filtersWereApplied() ? getFilters() : null, getAttributes(), getReferenceBaseForIndel());
     }