diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index d44e41797..406c49918 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -86,9 +86,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
         Set<String> samples = SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
 
-        String[] annotationsToUse = {};
-        String[] annotationClassesToUse = { "Standard" };
-        engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
+        ArrayList<String> annotationClassesToUse = new ArrayList<String>();
+        annotationClassesToUse.add("Standard");
+        engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, new ArrayList<String>());
 
         if ( SET_KEY.toLowerCase().equals("null") )
             SET_KEY = null;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
index 24eee7f4c..b0bd64e5b 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
@@ -226,7 +226,9 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VariantContext>, Link
         }
 
         //instanciate the VariantAnnotatorEngine
-        engine = new VariantAnnotatorEngine(getToolkit(), new String[] { }, new String[] { "GenomicAnnotation" });
+        ArrayList<String> annotationsToUse = new ArrayList<String>();
+        annotationsToUse.add("GenomicAnnotation");
+        engine = new VariantAnnotatorEngine(getToolkit(), new ArrayList<String>(), annotationsToUse);
         engine.setOneToMany( Boolean.TRUE.equals( ONE_TO_MANY ) );
         engine.setRequestedColumns(SELECT_COLUMNS);
         engine.setJoinTables(joinTables);