diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
index 584c13c71..5bff21632 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
@@ -314,9 +314,15 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
             for (final String sample : validation.getSampleNames()) {
                 final Genotype.Type truth = validation.getGenotype(sample).getType();
                 sampleStats.incrValue(sample, truth, called);
-                if ( (truth == Genotype.Type.HOM_VAR || truth == Genotype.Type.HET) && called == Genotype.Type.NO_CALL ) {
-                    if ( PRINT_INTERESTING_SITES && super.getVEWalker().printInterestingSites() )
-                        ;//System.out.printf("%s: HM3 FN => %s%n", group, validation);
+
+                // print out interesting sites
+                if ( PRINT_INTERESTING_SITES && super.getVEWalker().gcLog != null ) {
+                    if ( (truth == Genotype.Type.HOM_VAR || truth == Genotype.Type.HET) && called == Genotype.Type.NO_CALL ) {
+                        super.getVEWalker().gcLog.printf("%s FN %s%n", group, validation);
+                    }
+                    if ( (called == Genotype.Type.HOM_VAR || called == Genotype.Type.HET) && truth == Genotype.Type.HOM_REF ) {
+                        super.getVEWalker().gcLog.printf("%s FP %s%n", group, validation);
+                    }
                 }
             }
         }
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 efb56b372..1d2c33ccb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -54,6 +54,7 @@ import org.broadinstitute.sting.utils.text.XReadLines;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.OutputStreamWriter;
+import java.io.PrintStream;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 import java.util.*;
@@ -158,6 +159,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     @Argument(shortName="outputVCF", fullName="InterestingSitesVCF", doc="If provided, interesting sites emitted to this vcf and the INFO field annotated as to why they are interesting", required=false)
     protected String outputVCF = null;
 
+    @Argument(shortName="gcLog", fullName="GenotypeCocordanceLog", doc="If provided, sites with genotype concordance problems (e.g., FP and FNs) will be emitted ot this file", required=false)
+    protected PrintStream gcLog = null;
+
     private static double NO_MIN_QUAL_SCORE = -1.0;
     @Argument(shortName = "Q", fullName="minPhredConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
     public double minQualScore = NO_MIN_QUAL_SCORE;