diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 23ec0fa70..7a1381b62 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -565,15 +566,23 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         // can't know stop location for deletions from reference
 
         DBCursor cursor = mongoCollection.find(query);
-        Map<String,DBObject> results = new HashMap<String,DBObject>();
-        Map<String,ArrayList<Genotype>> genotypes = new HashMap<String,ArrayList<Genotype>>();
+        Map<Pair<String,List<Allele>>,DBObject> results = new HashMap<Pair<String,List<Allele>>,DBObject>();
+        Map<Pair<String,List<Allele>>,List<Genotype>> genotypes = new HashMap<Pair<String,List<Allele>>,List<Genotype>>();
+
         while(cursor.hasNext()) {
             DBObject oneResult = cursor.next();
 
-            String type = (String)oneResult.get("type");
-            results.put(type, oneResult);
-
             String sample = (String)oneResult.get("sample");
+            String sourceROD = (String)oneResult.get("sourceROD");
+
+            ArrayList<Allele> alleles = new ArrayList<Allele>();
+            BasicDBObject allelesInDb = (BasicDBObject)oneResult.get("alleles");
+            for (Object alleleInDb : allelesInDb.values()) {
+                String rawAllele = (String)alleleInDb;
+                boolean isRef = rawAllele.contains("*");
+                String allele = rawAllele.replace("*", "");
+                alleles.add(Allele.create(allele, isRef));
+            }
 
             BasicDBObject genotypeInDb = (BasicDBObject)oneResult.get("genotype");
             Double genotypeError = (Double)genotypeInDb.get("error");
@@ -598,24 +607,20 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
             Genotype genotype = new Genotype(sample, genotypeAlleles, genotypeError);
 
-            if (!genotypes.containsKey(type))
-                genotypes.put(type, new ArrayList<Genotype>());
+            // primary key to uniquely identify variant
+            Pair<String, List<Allele>> sourceRodAllelePair = new Pair<String, List<Allele>>(sourceROD, alleles);
 
-            Collection<Genotype> genotypesByType = genotypes.get(type);
-            genotypesByType.add(Genotype.modifyAttributes(genotype, genotypeAttributes));
+            if (!genotypes.containsKey(sourceRodAllelePair))
+                genotypes.put(sourceRodAllelePair, new ArrayList<Genotype>());
+
+            Collection<Genotype> genotypesBySourceROD = genotypes.get(sourceRodAllelePair);
+            genotypesBySourceROD.add(Genotype.modifyAttributes(genotype, genotypeAttributes));
+
+            results.put(sourceRodAllelePair, oneResult);
         }
 
-        for (String type : results.keySet()) {
-            DBObject result = results.get(type);
-
-            ArrayList<Allele> alleles = new ArrayList<Allele>();
-            BasicDBObject allelesInDb = (BasicDBObject)result.get("alleles");
-            for (Object alleleInDb : allelesInDb.values()) {
-                String rawAllele = (String)alleleInDb;
-                boolean isRef = rawAllele.contains("*");
-                String allele = rawAllele.replace("*", "");
-                alleles.add(Allele.create(allele, isRef));
-            }
+        for (Pair<String, List<Allele>> sourceRodAllelePair : results.keySet()) {
+            DBObject result = results.get(sourceRodAllelePair);
 
             Map<String, Object> attributes = new TreeMap<String, Object>();
             BasicDBList attrsInDb = (BasicDBList)result.get("attributes");
@@ -638,11 +643,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             String id = (String)result.get("id");
             Double error = (Double)result.get("error");
 
-            VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, alleles);
+            VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, sourceRodAllelePair.getSecond());
 
             builder.id(id);
             builder.log10PError(error);
-            builder.genotypes(genotypes.get(type));
+            builder.genotypes(genotypes.get(sourceRodAllelePair));
             builder.attributes(attributes);
             builder.filters(filters);