diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
index e06798fd2..293e4b21a 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -150,7 +150,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     @Test public void uniqueSNPs() {
         // parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s
-        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "e5ea6ac3905bd9eeea1a2ef5d2cb5af7", true);
+        //both of these files have the YRI trio and merging of duplicate samples without priority must be specified with UNSORTED merge type
+        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "e5ea6ac3905bd9eeea1a2ef5d2cb5af7", true);
     }
 
     @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "def52bcd3942bbe39cd7ebe845c4f206"); }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
index beb453b7b..aa69693b8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
@@ -208,14 +208,25 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
             logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option");
 
         validateAnnotateUnionArguments();
-        if ( PRIORITY_STRING == null && genotypeMergeOption == null) {
-            genotypeMergeOption = GATKVariantContextUtils.GenotypeMergeType.UNSORTED;
+
+        final boolean sampleNamesAreUnique = SampleUtils.verifyUniqueSamplesNames(vcfRods);
+
+        if (genotypeMergeOption == null) {
+            if (!sampleNamesAreUnique)
+                throw new UserException("Duplicate sample names were discovered but no genotypemergeoption was supplied. " +
+                    "To combine samples without merging specify --genotypemergeoption UNIQUIFY. Merging duplicate samples " +
+                    "without specified priority is unsupported, but can be achieved by specifying --genotypemergeoption UNSORTED.");
+            else
+                genotypeMergeOption = GATKVariantContextUtils.GenotypeMergeType.UNSORTED;
+        }
+
+        if ( PRIORITY_STRING == null && genotypeMergeOption == GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE) {
             //PRIORITY_STRING = Utils.join(",", vcfRods.keySet());  Deleted by Ami (7/10/12)
             logger.info("Priority string is not provided, using arbitrary genotyping order: "+priority);
         }
 
         if (genotypeMergeOption == GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE &&
-                !SampleUtils.verifyUniqueSamplesNames(vcfRods))
+                !sampleNamesAreUnique)
             throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered.");
 
         samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption);