diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 528a28d9e..7272b36c8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -116,6 +116,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
 
     @Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false)
     protected String[] KNOWN_NAMES = {rodDbSNP.STANDARD_DBSNP_TRACK_NAME};
+    private Set<String> uniqueKnownNames = new HashSet<String>();
 
     @Argument(shortName="sample", doc="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context", required=false)
     protected String[] SAMPLES = {};
@@ -260,13 +261,13 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
             if ( d.getName().startsWith("eval") ) {
                 evalNames.add(d.getName());
-            } else if ( d.getName().startsWith(rodDbSNP.STANDARD_DBSNP_TRACK_NAME) ) {
+            } else if ( d.getName().startsWith("comp") ) {
+                compNames.add(d.getName());
+            } else if ( d.getName().startsWith(rodDbSNP.STANDARD_DBSNP_TRACK_NAME) || d.getName().startsWith("hapmap") ) {
                 // it feels like overkill (i.e. too much output) to include the dbsnp track as
                 //  truth given that it's also used in the known/novel stratification.  If this
                 //  becomes useful for some reason, uncomment this line...
-                //compNames.add(d.getName());
-            } else if ( d.getName().startsWith("hapmap") || d.getName().startsWith("comp") ) {
-                compNames.add(d.getName());
+                uniqueKnownNames.add(d.getName());
             } else {
                 logger.info("Not evaluating ROD binding " + d.getName());
             }
@@ -571,6 +572,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         if ( tracker != null ) {
             bindVariantContexts(bindings, evalNames, tracker, context, false);
             bindVariantContexts(bindings, compNames, tracker, context, true);
+            bindVariantContexts(bindings, uniqueKnownNames, tracker, context, true);
         }
         return bindings;
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 331a48a99..e6b212e0e 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -18,8 +18,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        expectations.put("-L 1:1-10,000,000", "f44a2c9057a78349e1d3ccec327d3343");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "e8c5107015e5926aa647e274cb58bff6");
+        expectations.put("-L 1:1-10,000,000", "5ea9dd109c45c47243f40af759b36d09");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "8b126d445eaec0263d2af6fbfea5ad8b");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -39,8 +39,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
                 " -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
 
-        expectations.put("", "49a723e6e77a45a4fb0a46890d66806b");
-        expectations.put(" -known comp_hapmap -known dbsnp", "11e2a3ae77b3ce4b659baa832388f920");
+        expectations.put("", "1bc8126366117045bb08872e098502af");
+        expectations.put(" -known comp_hapmap -known dbsnp", "1bc8126366117045bb08872e098502af");
         expectations.put(" -known comp_hapmap", "11e2a3ae77b3ce4b659baa832388f920");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
@@ -59,7 +59,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
         WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
                 2,
-                Arrays.asList("d8b14bc334a8c4f3cd5462839f5a3ef2", "a3ce1d70d8ae3874807e9d61994d42af"));
+                Arrays.asList("cd4813cc4bcce0f8f81d42bcde11f7ce", "a3ce1d70d8ae3874807e9d61994d42af"));
         executeTest("testVEWriteVCF", spec);
     }
 }