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 7272b36c8..cd996ff18 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -116,7 +116,6 @@ 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 = {};
@@ -264,10 +263,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
             } 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...
-                uniqueKnownNames.add(d.getName());
+                compNames.add(d.getName());
             } else {
                 logger.info("Not evaluating ROD binding " + d.getName());
             }
@@ -466,8 +462,11 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                             break;
                         case 2:
                             VariantContext comp = vcs.get(group.compTrackName);
-                            if ( comp != null && minCompQualScore != NO_MIN_QUAL_SCORE && comp.getNegLog10PError() < (minCompQualScore / 10.0))
-                                comp = null;                            
+                            if ( comp != null &&
+                                    minCompQualScore != NO_MIN_QUAL_SCORE &&
+                                    comp.hasNegLog10PError() &&
+                                    comp.getNegLog10PError() < (minCompQualScore / 10.0) )
+                                comp = null;
                             String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context );
                             if ( interesting != null ) interestingReasons.add(interesting);
                             break;
@@ -523,7 +522,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         if ( vc == null )
             return true;
 
-        if ( minQualScore != NO_MIN_QUAL_SCORE && vc.getNegLog10PError() < (minQualScore / 10.0)) {
+        if ( minQualScore != NO_MIN_QUAL_SCORE &&
+                vc.hasNegLog10PError() &&
+                vc.getNegLog10PError() < (minQualScore / 10.0) ) {
             //System.out.printf("exclude %s%n", vc);
             return false;
         }
@@ -572,7 +573,6 @@ 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/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java b/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
index 9f636c8ab..ac810b228 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
@@ -5,9 +5,7 @@ import org.broadinstitute.sting.playground.utils.report.utils.Node;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
-import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 
 
 /**
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 e6b212e0e..d0da7ac09 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", "5ea9dd109c45c47243f40af759b36d09");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "8b126d445eaec0263d2af6fbfea5ad8b");
+        expectations.put("-L 1:1-10,000,000", "bb96e002225df21a84ba7c72613cc67a");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "7427803b4121665e130c76191f862231");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -39,9 +39,10 @@ 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("", "1bc8126366117045bb08872e098502af");
-        expectations.put(" -known comp_hapmap -known dbsnp", "1bc8126366117045bb08872e098502af");
-        expectations.put(" -known comp_hapmap", "11e2a3ae77b3ce4b659baa832388f920");
+        String matchingMD5 = "920940d4006d5d140183f3ba35cafe00";
+        expectations.put("", matchingMD5);
+        expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
+        expectations.put(" -known comp_hapmap", "ae9ab5a1556e773b3b1ba80453b14eda");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs2 = entry.getKey();
@@ -59,7 +60,7 @@ 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("cd4813cc4bcce0f8f81d42bcde11f7ce", "a3ce1d70d8ae3874807e9d61994d42af"));
+                Arrays.asList("40fca380c2e768cfff5febefc4a73aa0", "a3ce1d70d8ae3874807e9d61994d42af"));
         executeTest("testVEWriteVCF", spec);
     }
 }