diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index 10b96fbeb..4ea4e601a 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -337,10 +337,10 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.isFiltered();
     }
 
-    public boolean hasFilteringCodes() {
-        assertNotNull();
-        return mCurrentRecord.hasFilteringCodes();
-    }
+//    public boolean hasFilteringCodes() {
+//        assertNotNull();
+//        return mCurrentRecord.hasFilteringCodes();
+//    }
 
     public String getFilterString() {
         assertNotNull();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
index d27ca4a35..b1a53a885 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
@@ -26,7 +26,7 @@ public class SimpleVenn implements ConcordanceType {
         sample2 = iter.next();
     }
 
-    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref) {
+    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref ) {
 
         Genotype call1 = samplesToRecords.get(sample1);
         if ( call1 != null && call1.isNoCall() )
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index 20d60e52f..10b2c3e89 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -350,9 +350,9 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
         return !codes[0].equals(UNFILTERED) && !codes[0].equals(PASSES_FILTERS);
     }
 
-    public boolean hasFilteringCodes() {
-        return mFilterString != null;
-    }
+//    public boolean hasFilteringCodes() {
+//        return mFilterString != null;
+//    }
 
     public String getFilterString() {
         return mFilterString;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
index 25ee85e87..ffaeaec52 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.*;
 
 import java.util.*;
@@ -140,7 +141,7 @@ public class VCFUtils {
         double totalFreq = 0.0;
         int freqsSeen = 0;
         String id = null;
-        String filter = null;
+        List<String> filters = new ArrayList<String>();
 
         for ( RodVCF rod : rods ) {
             List<VCFGenotypeRecord> myGenotypes = rod.getVCFGenotypeRecords();
@@ -173,8 +174,8 @@ public class VCFUtils {
             if ( rod.getID() != null )
                 id = rod.getID();
 
-            if ( rod.hasFilteringCodes() )
-                filter = rod.getFilterString();
+            if ( rod.isFiltered() )
+                filters.add(rod.getFilterString());
         }
 
         Map<String, String> infoFields = new HashMap<String, String>();
@@ -193,7 +194,7 @@ public class VCFUtils {
                 (id != null ? id : "."),
                 params.getAlternateBases(),
                 maxConfidence,
-                (filter != null ? filter : "."),
+                filters.size() == 0 ? "0" : Utils.join(";", filters),
                 infoFields,
                 params.getFormatString(),
                 params.getGenotypesRecords());
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
index 120027cc3..2e5ed1687 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
@@ -14,7 +14,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testSimpleVenn() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn", 1,
-                Arrays.asList("f4c4b7430f0e293c27ce38cb89b9338b"));
+                Arrays.asList("c0376dcd60f1741eac2917f10b4bb7a4"));
         executeTest("testSimpleVenn", spec);
     }
 
@@ -22,7 +22,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testSNPConcordance() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1,
-                Arrays.asList("f754e046bc0fa3a4b3430061e412ef0d"));
+                Arrays.asList("ffc13b79f6a18158f63cc9a8ee968f32"));
         executeTest("testSNPConcordance", spec);
     }
 
@@ -30,7 +30,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testNWayVenn() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -B set3,VCF," + validationDataLocation + "CEU.sample.vcf -CT NWayVenn", 1,
-                Arrays.asList("86d2342fabc8c0916a6d42a29f750ea2"));
+                Arrays.asList("39717fb57526e54540e803a1f9c5d31b"));
         executeTest("testNWayVenn", spec);
     }
 
@@ -38,7 +38,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testMulti() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1,
-                Arrays.asList("6fbe00cb68d2cdc59dfcb79024fd9893"));
+                Arrays.asList("0b5b0c9ce7e21d1d2c38ebaad7765017"));
         executeTest("testMulti", spec);
     }