diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 22e5bd78a..2486d57ab 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -28,9 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.genotyper;
 import org.apache.log4j.Logger;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -41,7 +39,6 @@ import java.io.PrintStream;
 
 public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
-    private boolean DEBUGOUT = false;
     private boolean SIMPLE_GREEDY_GENOTYPER = false;
     private static final double[] log10Cache;
     private static final double[] jacobianLogTable;
@@ -330,11 +327,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
                 qual = -1.0 * Math.log10(1.0 - chosenGenotype);
             }
 
-            HashMap<String, Object> attributes = new HashMap<String, Object>(g.getAttributes());
-            attributes.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
-            attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.GLsToPLs(likelihoods));
-
-            calls.put(sample, new Genotype(sample, myAlleles, qual, null, attributes, false));
+            calls.put(sample, new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false));
 
         }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
index 642ca1106..c466341b6 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -28,9 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.genotyper;
 import org.apache.log4j.Logger;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -121,11 +119,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
                 myAlleles.add(altAllele);
             }
 
-            HashMap<String, Object> attributes = new HashMap<String, Object>(g.getAttributes());
-            attributes.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
-            attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.GLsToPLs(g.getLikelihoods().getAsVector()));
-
-            calls.put(sample, new Genotype(sample, myAlleles, AFbasedGenotype.second, null, attributes, false));
+            calls.put(sample, new Genotype(sample, myAlleles, AFbasedGenotype.second, null, g.getAttributes(), false));
         }
 
         return calls;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 7d6a26e62..120a28d02 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -144,7 +144,12 @@ public class UnifiedGenotyperEngine {
     public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
         Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
         VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
-        return vc == null ? null : calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc);
+        if ( vc == null )
+            return null;
+
+        VariantCallContext vcc = calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc);
+        vcc.vc = GLsToPLs(vcc.vc);
+        return vcc;
     }
 
     /**
@@ -157,7 +162,8 @@ public class UnifiedGenotyperEngine {
      */
     public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
         Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
-        return calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
+        VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
+        return GLsToPLs(vc);
     }
 
     private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, StratifiedAlignmentContext> stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType type) {
@@ -214,6 +220,20 @@ public class UnifiedGenotyperEngine {
                 null);
     }
 
+    private static VariantContext GLsToPLs(VariantContext vc) {
+        if ( vc == null )
+            return null;
+
+        HashMap<String, Genotype> calls = new HashMap<String, Genotype>();
+        for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
+            HashMap<String, Object> attributes = new HashMap<String, Object>(genotype.getValue().getAttributes());
+            attributes.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
+            attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.GLsToPLs(genotype.getValue().getLikelihoods().getAsVector()));
+            calls.put(genotype.getKey(), Genotype.modifyAttributes(genotype.getValue(), attributes));
+        }
+        return VariantContext.modifyGenotypes(vc, calls);
+    }
+
     /**
      * Compute genotypes at a given locus.
      *
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
index c875865e9..4b65c8b66 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
@@ -153,7 +153,6 @@ public class UnifiedGenotyperV2 extends LocusWalker<VariantCallContext, UnifiedG
         }
 
         // FORMAT and INFO fields
-        // TODO: if only outputting GLs, change this to the GL version
         headerInfo.addAll(VCFUtils.getSupportedHeaderStrings(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY));
 
         // FILTER fields