diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
index 199126a7c..6faba48eb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
@@ -62,8 +62,7 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
             mongoCollection.ensureIndex("stop");
 
             // set up primary key
-            mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1), new BasicDBObject("unique", 1));
-
+            mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
         }
         catch (MongoException e) {}
         catch (java.net.UnknownHostException e) {}
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 2797426cb..23ec0fa70 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
@@ -562,9 +562,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         BasicDBObject query = new BasicDBObject();
         query.put("contig", contig);
         query.put("start", start);
-        query.put("stop", stop);
-        //query.put("sample", "NA12878");    // TODO: remove kluge
-        query.put("sample", new BasicDBObject("$ne", "NA12878"));    // TODO: remove kluge
+        // can't know stop location for deletions from reference
 
         DBCursor cursor = mongoCollection.find(query);
         Map<String,DBObject> results = new HashMap<String,DBObject>();