diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java
index 7bfd72155..6a6ac9032 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java
@@ -11,6 +11,7 @@ import java.util.Set;
  * To change this template use File | Settings | File Templates.
  */
 class MultiSampleConcordanceSet {
+    private boolean treatTruthOnlyAsFalseNegative;
     private int minimumDepthForTest;
     private HashSet<VCFConcordanceCalculator> concordanceSet;
     private Set<String> cachedSampleNames;
@@ -18,14 +19,17 @@ class MultiSampleConcordanceSet {
     private long truthOnlyVariantSites;
     private long variantOnlySites;
     private long overlappingSites;
+    private int genotypeQuality;
 
-    public MultiSampleConcordanceSet(int minDepth) {
+    public MultiSampleConcordanceSet(int minDepth, boolean assumeRef, int genotypeQuality) {
         concordanceSet = new HashSet<VCFConcordanceCalculator>();
         truthOnlySites = 0l;
         truthOnlyVariantSites = 0l;
         variantOnlySites = 0l;
         overlappingSites = 0l;
         minimumDepthForTest = minDepth;
+        treatTruthOnlyAsFalseNegative = assumeRef;
+        this.genotypeQuality = genotypeQuality;
     }
 
     public boolean hasBeenInstantiated() {
@@ -35,7 +39,7 @@ class MultiSampleConcordanceSet {
     public void instantiate(Set<String> samples) {
         cachedSampleNames = samples;
         for ( String s : samples ) {
-            concordanceSet.add(new VCFConcordanceCalculator(s,minimumDepthForTest));
+            concordanceSet.add(new VCFConcordanceCalculator(s,minimumDepthForTest,genotypeQuality));
         }
     }
 
@@ -49,6 +53,11 @@ class MultiSampleConcordanceSet {
             truthOnlySites++;
             if ( info.isVariantSite() ) {
                 truthOnlyVariantSites++;
+                if ( treatTruthOnlyAsFalseNegative ) {
+                    for ( VCFConcordanceCalculator concordance : concordanceSet ) {
+                        concordance.updateTruthOnly(info);
+                    }
+                }
             }
         } else {
             variantOnlySites++;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
index 4e6588805..5922055cb 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
@@ -28,15 +28,20 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 public class MultiSampleConcordanceWalker extends RodWalker< LocusConcordanceInfo, MultiSampleConcordanceSet > {
     @Argument(fullName="noLowDepthLoci", shortName="NLD", doc="Do not use loci in analysis where the variant depth (as specified in the VCF) is less than the given number; "+
             "DO NOT USE THIS IF YOUR VCF DOES NOT HAVE 'DP' IN THE FORMAT FIELD", required=false) private int minDepth = -1;
+    @Argument(fullName="genotypeConfidence", shortName="GC", doc="The quality score for genotypes below which to count genotyping as a no-call", required=false)
+    int genotypeQuality = 0;
     @Argument(fullName = "ignoreKnownSites", shortName = "novel", doc="Only run concordance over novel sites (sites marked in the VCF as being in dbSNP or Hapmap 2 or 3)", required=false )
     boolean ignoreKnownSites = false;
+    @Argument(fullName="missingLocusAsConfidentRef", shortName="assumeRef", doc="Assume a missing locus in the variant VCF is a confident ref call with sufficient depth"+
+    "across all samples. Default: Missing locus = no call", required=false)
+    boolean assumeRef = false;
 
     public void initialize() {
 
     }
 
     public MultiSampleConcordanceSet reduceInit() {
-        return new MultiSampleConcordanceSet(minDepth);
+        return new MultiSampleConcordanceSet(minDepth,assumeRef,genotypeQuality);
     }
 
     public LocusConcordanceInfo map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext c) {
@@ -97,7 +102,7 @@ public class MultiSampleConcordanceWalker extends RodWalker< LocusConcordanceInf
     }
 
     public void onTraversalDone(MultiSampleConcordanceSet cSet) {
-        out.printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s%n","Sample_ID","Ignored_due_to_depth","Concordant_Refs","Concordant_Homs","Concordant_Hets","Homs_called_het","Het_called_homs","False_Positives","False_Negatives_Due_To_Ref_Call","False_Negatives_Due_To_No_Call");
+        out.printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s%n","Sample_ID","Ignored_due_to_depth","Concordant_Refs","Concordant_Homs","Concordant_Hets","Correct_But_Low_Genotype_Qual","Homs_called_het","Het_called_homs","False_Positives","False_Negatives_Due_To_Ref_Call","False_Negatives_Due_To_No_Call");
         for ( VCFConcordanceCalculator sample : cSet.getConcordanceSet() ) {
             out.print(String.format("%s%n",sample));
         }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java
index 5f9d401bb..e5c0ae3a4 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java
@@ -1,8 +1,10 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
 
+import java.util.Arrays;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -14,40 +16,56 @@ import java.util.Set;
  * To change this template use File | Settings | File Templates.
  */
 class VCFConcordanceCalculator {
+
     private int minimumDepthForUpdate;
+    private int minimumGenotypeQuality;
     private String name;
     private Set<GenomeLoc> falsePositiveLoci;
     private Set<GenomeLoc> falseNegativeLoci;
     private Set<GenomeLoc> falseNegativeLociDueToNoCall;
     private Set<GenomeLoc> hetsCalledHoms;
     private Set<GenomeLoc> homsCalledHets;
+    private Set<GenomeLoc> nonConfidentGenotypeCalls;
     private Set<GenomeLoc> concordantHomCalls;
     private Set<GenomeLoc> concordantHetCalls;
     private Set<GenomeLoc> concordantGenotypeReferenceCalls;
     private Set<GenomeLoc> chipNoCalls;
     private Set<GenomeLoc> ignoredDueToDepth;
 
-    public VCFConcordanceCalculator(String sampleName, int minimumDepth) {
+    public VCFConcordanceCalculator(String sampleName, int minimumDepth, int minGenQual) {
         name = sampleName;
         falseNegativeLoci = new HashSet<GenomeLoc>();
         falseNegativeLociDueToNoCall = new HashSet<GenomeLoc>();
         falsePositiveLoci = new HashSet<GenomeLoc>();
         hetsCalledHoms = new HashSet<GenomeLoc>();
         homsCalledHets = new HashSet<GenomeLoc>();
+        nonConfidentGenotypeCalls = new HashSet<GenomeLoc>();
         concordantHomCalls = new HashSet<GenomeLoc>();
         concordantHetCalls = new HashSet<GenomeLoc>();
         concordantGenotypeReferenceCalls = new HashSet<GenomeLoc>();
         chipNoCalls = new HashSet<GenomeLoc>();
         ignoredDueToDepth = new HashSet<GenomeLoc>();
         minimumDepthForUpdate = minimumDepth;
+        minimumGenotypeQuality = minGenQual;
     }
 
     public void update(LocusConcordanceInfo info) {
         compareGenotypes(info.getTruthGenotype(name), info.getVariantGenotype(name), info.getLoc(), info.getReferenceBase() );
     }
 
+    public void updateTruthOnly(LocusConcordanceInfo info) {
+        if ( info.getTruthGenotype(name).isVariant( (char) info.getReferenceBase() ) ) {
+            falseNegativeLoci.add(info.getLoc());
+        } else {
+            concordantGenotypeReferenceCalls.add(info.getLoc());
+        }
+    }
+
     public String toString() {
-        return String.format("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d",name,ignoredDueToDepth.size(),concordantGenotypeReferenceCalls.size(),concordantHomCalls.size(),concordantHetCalls.size(),homsCalledHets.size(),hetsCalledHoms.size(),falsePositiveLoci.size(),falseNegativeLoci.size(),falseNegativeLociDueToNoCall.size());
+        return String.format("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d",name,ignoredDueToDepth.size(),
+                concordantGenotypeReferenceCalls.size(),concordantHomCalls.size(),concordantHetCalls.size(),nonConfidentGenotypeCalls.size(),
+                homsCalledHets.size(),hetsCalledHoms.size(),falsePositiveLoci.size(),falseNegativeLoci.size(),
+                falseNegativeLociDueToNoCall.size());
     }
 
     private void compareGenotypes(VCFGenotypeRecord truth, VCFGenotypeRecord call, GenomeLoc loc, byte ref) {
@@ -78,14 +96,21 @@ class VCFConcordanceCalculator {
     }
 
     private void checkGenotypeCall( VCFGenotypeRecord truth, VCFGenotypeRecord call, GenomeLoc loc ) {
-        if ( truth.isHet() && call.isHom() ) {
-            hetsCalledHoms.add(loc);
-        } else if ( truth.isHom() && call.isHet() ) {
-            homsCalledHets.add(loc);
-        } else if (  ( truth.isHet() && call.isHet()  ) ) {
-            concordantHetCalls.add(loc);
-        } else if ( truth.isHom() && call.isHom() ) { // be extra careful
-            concordantHomCalls.add(loc);
+        if ( ! call.isFiltered() && 10*call.getNegLog10PError() > minimumGenotypeQuality) {
+
+            if ( truth.isHet() && call.isHom() ) {
+                hetsCalledHoms.add(loc);
+            } else if ( truth.isHom() && call.isHet() ) {
+                homsCalledHets.add(loc);
+            } else if (  ( truth.isHet() && call.isHet()  ) ) {
+                concordantHetCalls.add(loc);
+            } else if ( truth.isHom() && call.isHom() ) { // be extra careful
+                concordantHomCalls.add(loc);
+            }
+
+        } else {
+            
+            nonConfidentGenotypeCalls.add(loc);
         }
 
     }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.java
new file mode 100644
index 000000000..d398de5eb
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.java
@@ -0,0 +1,42 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.vcftools;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
+import java.lang.Long;
+
+/**
+ * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
+ *
+ * @Author chartl
+ * @Date Jan 29, 2010
+ */
+public abstract class SimpleVCFIntersectWalker extends RodWalker<VCFRecordPair,Long>{
+
+    public void initialize() {
+
+    }
+
+    public Long reduceInit() {
+        return 0l;
+    }
+
+    public VCFRecordPair map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return null;
+    }
+
+    public Long reduce(VCFRecordPair records, long prevReduce) {
+        return 0l;
+    }
+
+    public void onTraversalDone(long finalReduce) {
+        return;
+    }
+}
+
+class VCFRecordPair {
+    public VCFRecord rec1;
+    public VCFRecord rec2;
+}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
index 02c55858c..814b02542 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
@@ -193,6 +193,10 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked {
         return true;
     }
 
+    public boolean isFiltered() {
+        return ( mFields.get(FILTER_KEY) != null && ! mFields.get(FILTER_KEY).equals("0"));
+    }
+
     public int getPloidy() {
         return 2;
     }