diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
index 4f33378f8..2c0c9b42d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
@@ -174,7 +174,8 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
     {
         // Print RESULT data for confident calls
         //if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asTabularString()); }
-        out.print(alleleFreq.asTabularString()); 
+        //out.print(alleleFreq.asTabularString()); 
+        if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asGFFString()); }
 
         if (this.num_loci_total % 1000 == 0) { printMetrics(); }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
index 295d0fd08..26e5c93cc 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -353,7 +353,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
     public Integer reduce(AlleleFrequencyEstimate alleleFreq, Integer sum) 
     {
         // Print RESULT data for confident calls
-        if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asTabularString()); }
+        if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asGFFString()); }
         return 0;
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
index bd1646dc2..ef2743fd4 100755
--- a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
@@ -29,6 +29,20 @@ public class AlleleFrequencyEstimate {
         this.notes = "";
     }
 
+    public String asGFFString()
+    {
+        String[] tokens;
+        tokens = location.split(":");
+        return String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\tREF \"%c\"\t;\tALT \"%c\"\t;\tFREQ %f\n",
+                               tokens[0],
+                               tokens[1],
+                               tokens[1],
+                               lodVsRef,
+                               ref,
+                               alt,
+                               qhat);
+    }
+
     public String asTabularString() {
         return String.format("RESULT %s %c %c %f %f %f %f %d %s\n",
 	                                        location,