diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 7062f17e5..3e3b29a7f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -234,16 +234,47 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         if (minimumN > 1 && (vcs.size() - numFilteredRecords < minimumN))
             return 0;
         
-        List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
+        List<VariantContext> preMergedVCs = new ArrayList<VariantContext>();
         Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
         // iterate over the types so that it's deterministic
         for ( VariantContext.Type type : VariantContext.Type.values() ) {
             if ( VCsByType.containsKey(type) )
-                mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
+                preMergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
                         priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
                         SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
         }
 
+        List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
+        // se have records merged but separated by type. If a particular record is for example a snp but all alleles are a subset of an existing mixed record,
+        // we will still merge those records.
+        if (preMergedVCs.size() > 1) {
+            for (VariantContext vc1 : preMergedVCs) {
+                VariantContext newvc = vc1;
+                boolean merged = false;
+                for (int k=0; k < mergedVCs.size(); k++) {
+                    VariantContext vc2 = mergedVCs.get(k);
+
+                    if (VariantContextUtils.allelesAreSubset(vc1,vc2) || VariantContextUtils.allelesAreSubset(vc2,vc1)) {
+                        // all alleles of vc1 are contained in vc2 but they are of different type (say, vc1 is snp, vc2 is complex): try to merget v1 into v2
+                        List<VariantContext> vcpair = new ArrayList<VariantContext>();
+                        vcpair.add(vc1);
+                        vcpair.add(vc2);
+                        newvc = VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcpair,
+                                               priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
+                                               SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC);
+                        mergedVCs.set(k,newvc);
+                        merged = true;
+                        break;
+                    }
+                }
+                if (!merged)
+                    mergedVCs.add(vc1);
+            }
+        }
+        else {
+            mergedVCs = preMergedVCs;
+        }
+
         for ( VariantContext mergedVC : mergedVCs ) {
             // only operate at the start of events
             if ( mergedVC == null )
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 986d6305c..506bb3b33 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -663,6 +663,18 @@ public class VariantContextUtils {
         return merged;
     }
 
+    public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) {
+        // if all alleles of vc1 are a contained in alleles of vc2, return true
+        if (!vc1.getReference().equals(vc2.getReference()))
+            return false;
+
+        for (Allele a :vc1.getAlternateAlleles()) {
+            if (!vc2.getAlternateAlleles().contains(a))
+                return false;
+        }
+
+        return true;
+    }
     public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) {
         // see if we need to trim common reference base from all alleles
         boolean trimVC;