diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java
index 47d04b62e..441f503ed 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/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 int minimumDepthForTest;
     private HashSet<VCFConcordanceCalculator> concordanceSet;
     private Set<String> cachedSampleNames;
     private long truthOnlySites;
@@ -18,12 +19,13 @@ class MultiSampleConcordanceSet {
     private long variantOnlySites;
     private long overlappingSites;
 
-    public MultiSampleConcordanceSet() {
+    public MultiSampleConcordanceSet(int minDepth) {
         concordanceSet = new HashSet<VCFConcordanceCalculator>();
         truthOnlySites = 0l;
         truthOnlyVariantSites = 0l;
         variantOnlySites = 0l;
         overlappingSites = 0l;
+        minimumDepthForTest = minDepth;
     }
 
     public boolean hasBeenInstantiated() {
@@ -33,7 +35,7 @@ class MultiSampleConcordanceSet {
     public void instantiate(Set<String> samples) {
         cachedSampleNames = samples;
         for ( String s : samples ) {
-            concordanceSet.add(new VCFConcordanceCalculator(s));
+            concordanceSet.add(new VCFConcordanceCalculator(s,minimumDepthForTest));
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
index 7f132071a..4a7478cb1 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
@@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 /**
  * Created by IntelliJ IDEA.
@@ -25,13 +26,14 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
  */
 @Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="truth",type= RodVCF.class),@RMD(name="variants",type= RodVCF.class)})
 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;
     public void initialize() {
 
     }
 
     public MultiSampleConcordanceSet reduceInit() {
-        return new MultiSampleConcordanceSet();
+        return new MultiSampleConcordanceSet(minDepth);
     }
 
     public LocusConcordanceInfo map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext c) {
@@ -92,8 +94,7 @@ public class MultiSampleConcordanceWalker extends RodWalker< LocusConcordanceInf
     }
 
     public void onTraversalDone(MultiSampleConcordanceSet cSet) {
-        String[] header = {"Sample_ID","Concordant_Refs","Concordant_Vars","Homs_called_het","Het_called_homs","False_Positives","False_Negatives_Due_To_Ref_Call","False_Negatives_Due_To_No_Call"};
-        out.print(String.format("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s%n",header));
+        out.printf("%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_Vars","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/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java
index 8433487f2..fa12d950f 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java
@@ -14,6 +14,7 @@ import java.util.Set;
  * To change this template use File | Settings | File Templates.
  */
 class VCFConcordanceCalculator {
+    private int minimumDepthForUpdate;
     private String name;
     private Set<GenomeLoc> falsePositiveLoci;
     private Set<GenomeLoc> falseNegativeLoci;
@@ -23,8 +24,9 @@ class VCFConcordanceCalculator {
     private Set<GenomeLoc> concordantCalls;
     private Set<GenomeLoc> concordantGenotypeReferenceCalls;
     private Set<GenomeLoc> chipNoCalls;
+    private Set<GenomeLoc> ignoredDueToDepth;
 
-    public VCFConcordanceCalculator(String sampleName) {
+    public VCFConcordanceCalculator(String sampleName, int minimumDepth) {
         name = sampleName;
         falseNegativeLoci = new HashSet<GenomeLoc>();
         falseNegativeLociDueToNoCall = new HashSet<GenomeLoc>();
@@ -34,6 +36,8 @@ class VCFConcordanceCalculator {
         concordantCalls = new HashSet<GenomeLoc>();
         concordantGenotypeReferenceCalls = new HashSet<GenomeLoc>();
         chipNoCalls = new HashSet<GenomeLoc>();
+        ignoredDueToDepth = new HashSet<GenomeLoc>();
+        minimumDepthForUpdate = minimumDepth;
     }
 
     public void update(LocusConcordanceInfo info) {
@@ -41,10 +45,14 @@ class VCFConcordanceCalculator {
     }
 
     public String toString() {
-        return String.format("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d",name,concordantGenotypeReferenceCalls.size(),concordantCalls.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",name,ignoredDueToDepth.size(),concordantGenotypeReferenceCalls.size(),concordantCalls.size(),homsCalledHets.size(),hetsCalledHoms.size(),falsePositiveLoci.size(),falseNegativeLoci.size(),falseNegativeLociDueToNoCall.size());
     }
 
     private void compareGenotypes(VCFGenotypeRecord truth, VCFGenotypeRecord call, GenomeLoc loc, byte ref) {
+        if ( minimumDepthForUpdate > 0 && call.getReadCount() < minimumDepthForUpdate ) {
+            ignoredDueToDepth.add(loc);
+            return; // do not update; just go away
+        }
         if ( truth.isNoCall() ) {
             chipNoCalls.add(loc);
         } else if ( truth.isVariant(( char) ref) ) {