diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index b1d8dc91d..e710befc9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -134,7 +134,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
     protected VariantContextWriter vcfWriter = null;
 
     @Argument(shortName="genotypeMergeOptions", doc="Determines how we should merge genotype records for samples shared across the ROD files", required=false)
-    public VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
+    public VariantContextUtils.GenotypeMergeType genotypeMergeOption = null;
 
     @Argument(shortName="filteredRecordsMergeType", doc="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields", required=false)
     public VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
@@ -200,13 +200,13 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         } else
             logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option");
 
-        if ( PRIORITY_STRING == null ) {
+        validateAnnotateUnionArguments();
+        if ( PRIORITY_STRING == null && genotypeMergeOption == null) {
             genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED;
             //PRIORITY_STRING = Utils.join(",", vcfRods.keySet());  Deleted by Ami (7/10/12)
-            logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING);
+            logger.info("Priority string not provided, using arbitrary genotyping order: "+priority);
         }
 
-        validateAnnotateUnionArguments();
         samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
 
         if ( SET_KEY.toLowerCase().equals("null") )
@@ -228,16 +228,15 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null )
             throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes");
 
-        if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE )
+        if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ){
             priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
-        else
-            priority = new ArrayList<String>(rodNames);
+            if ( rodNames.size() != priority.size() )
+                throw new UserException.BadArgumentValue("rod_priority_list", "The priority list must contain exactly one rod binding per ROD provided to the GATK: rodNames=" + rodNames + " priority=" + priority);
 
-        if ( rodNames.size() != priority.size() )
-            throw new UserException.BadArgumentValue("rod_priority_list", "The priority list must contain exactly one rod binding per ROD provided to the GATK: rodNames=" + rodNames + " priority=" + priority);
+            if ( ! rodNames.containsAll(priority) )
+                throw new UserException.BadArgumentValue("rod_priority_list", "Not all priority elements provided as input RODs: " + PRIORITY_STRING);
+        }
 
-        if ( ! rodNames.containsAll(priority) )
-            throw new UserException.BadArgumentValue("rod_priority_list", "Not all priority elements provided as input RODs: " + PRIORITY_STRING);
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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 81959c998..614b234e9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -840,8 +840,11 @@ public class VariantContextUtils {
         if ( mergeOption == GenotypeMergeType.PRIORITIZE && priorityListOfVCs == null )
             throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list");
 
-        if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED )
+        if ( mergeOption == GenotypeMergeType.UNSORTED ){
+            if (priorityListOfVCs != null )
+                logger.info("Priority string was provided but is not used since GenotypeMergeType is UNSORTED");
             return new ArrayList<VariantContext>(unsortedVCs);
+        }
         else {
             ArrayList<VariantContext> sorted = new ArrayList<VariantContext>(unsortedVCs);
             Collections.sort(sorted, new CompareByPriority(priorityListOfVCs));