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 55790bd3f..199126a7c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
@@ -18,6 +18,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.io.File;
 import java.io.PrintStream;
 
 /**
@@ -38,6 +39,8 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
     protected Mongo mongo;
     protected DBCollection mongoCollection;
 
+    private String RODFileName;
+
     @Override
     public void initialize()
     {
@@ -46,15 +49,20 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
             DB mongoDb = mongo.getDB(MONGO_DB_NAME);
             mongoCollection = mongoDb.getCollection(MONGO_VC_COLLECTION);
 
+            RODFileName = input.getSource();
+            int lastSep = RODFileName.lastIndexOf(File.separator);
+            RODFileName = RODFileName.substring(lastSep + 1);
+
             // set up indices
             mongoCollection.ensureIndex("location");
             mongoCollection.ensureIndex("sample");
+            mongoCollection.ensureIndex("sourceROD");
             mongoCollection.ensureIndex("contig");
             mongoCollection.ensureIndex("start");
             mongoCollection.ensureIndex("stop");
 
             // set up primary key
-            mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1), new BasicDBObject("unique", 1));
+            mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1), new BasicDBObject("unique", 1));
 
         }
         catch (MongoException e) {}
@@ -82,7 +90,7 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
         for ( Feature feature : tracker.getValues(Feature.class, context.getLocation()) ) {
             if ( feature instanceof VariantContext ) {
                 VariantContext vc = (VariantContext) feature;
-                for (BasicDBObject vcForMongo : vc.toMongoDB()) {
+                for (BasicDBObject vcForMongo : vc.toMongoDB(RODFileName)) {
                     mongoCollection.insert(vcForMongo);
                 }
             }
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 155f5445b..ae88b4539 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1221,7 +1221,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
                 this.getGenotypes());
     }
 
-    public List<BasicDBObject> toMongoDB() {
+    public List<BasicDBObject> toMongoDB(String sourceROD) {
         List<BasicDBObject> vcDocs = new ArrayList<BasicDBObject>();
         for (Genotype genotype : this.getGenotypes()) {
             BasicDBObject vcDoc = new BasicDBObject();
@@ -1233,6 +1233,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
             vcDoc.put("error", this.getLog10PError());
             vcDoc.put("sample", genotype.getSampleName());
             vcDoc.put("source", this.getSource());
+            vcDoc.put("sourceROD", sourceROD);
             vcDoc.put("type", this.getType().toString());
 
             Integer alleleIndex = 0;