diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index ee4f77752..725097ddc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -277,8 +277,12 @@ public class VariantAnnotatorEngine {
             if ( expression.fieldName.equals("ID") ) {
                 if ( vc.hasID() )
                     infoAnnotations.put(expression.fullName, vc.getID());
+            } else if (expression.fieldName.equals("ALT")) {
+                infoAnnotations.put(expression.fullName, vc.getAlternateAllele(0).getDisplayString());
+
             } else if ( vc.hasAttribute(expression.fieldName) ) {
-                infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
+                    infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
+
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 879a46ab0..22ed95365 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -190,8 +190,8 @@ public class UnifiedGenotyperEngine {
                     final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
                     if ( vc != null )
                         results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap));
- //                   else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
-   //                     results.add(generateEmptyContext(tracker, refContext, null, rawContext));
+                    else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
+                        results.add(generateEmptyContext(tracker, refContext, null, rawContext));
 
                 }
             }