diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
index 81d714294..e3bef6bc5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
@@ -382,7 +382,7 @@ public final class GenotypeBuilder {
         else if ( filters.size() == 1 )
             return filter(filters.get(0));
         else
-            return filter(ParsingUtils.join(";", filters));
+            return filter(ParsingUtils.join(";", ParsingUtils.sortList(filters)));
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index f1bebaa30..843838972 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -147,6 +147,10 @@ public class VariantContextUtils {
 
                 attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts.size() == 1 ? alleleCounts.get(0) : alleleCounts);
                 attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs.size() == 1 ? alleleFreqs.get(0) : alleleFreqs);
+            } else {
+                // if there's no alt AC and AF shouldn't be present
+                attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
+                attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
             }
         }