diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 198ed84a3..641471920 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -82,7 +82,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
             listFiltersAndExit();
 
         // get the list of all sample names from the various VCF input rods
-        HashSet<String> samples = new HashSet<String>();
+        TreeSet<String> samples = new TreeSet<String>();
         VCFUtils.getUniquifiedSamplesFromRods(getToolkit(), samples, new HashMap<Pair<String, String>, String>());
 
         // add the non-VCF sample from the command-line, if applicable
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index ecb342d99..44057e592 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -50,7 +50,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("6903f8b31820ce7a56230b99f9a9309c"));
+                Arrays.asList("5c73e85a91bf8f8e9c47c445ec77233c"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("d9f623b69e20b9c6289562f123b867eb"));
+                Arrays.asList("2d3e220e96eb00c4c7bb2dbc8353d9bd"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b46f395864cb71b887d69342f56e7fdb"));
+                Arrays.asList("acef97201f2d17007dbdee6c639536ea"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("23928a3f79fd5d841505cdeaf342c8dc"));
+                Arrays.asList("2031599f8554d16342f53cb80fae296a"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }