diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
index 391b0202f..5f4e1b516 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.gatk.tools;
 
+import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import org.apache.log4j.BasicConfigurator;
@@ -47,6 +48,7 @@ import htsjdk.variant.vcf.VCFCodec;
 import htsjdk.variant.vcf.VCFHeader;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.variantcontext.VariantContextComparator;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
@@ -228,9 +230,9 @@ public class CatVariants extends CommandLineProgram {
 
         variant = parseVariantList(variant);
 
-        Comparator<Pair<Integer,File>> positionComparator = new PositionComparator();
+        Comparator<Pair<VariantContext,File>> positionComparator = new PositionComparator(ref.getSequenceDictionary());
 
-        Queue<Pair<Integer,File>> priorityQueue;
+        Queue<Pair<VariantContext,File>> priorityQueue;
         if (assumeSorted)
             priorityQueue = new LinkedList<>();
         else
@@ -244,7 +246,7 @@ public class CatVariants extends CommandLineProgram {
                 return 1;
 
             if (assumeSorted){
-                priorityQueue.add(new Pair<>(0,file));
+                priorityQueue.add(new Pair<VariantContext,File>(null,file));
             }
             else{
                 if (!file.exists()) {
@@ -257,9 +259,8 @@ public class CatVariants extends CommandLineProgram {
                     continue;
                 }
                 VariantContext vc = it.next();
-                int firstPosition = vc.getStart();
                 reader.close();
-                priorityQueue.add(new Pair<>(firstPosition,file));
+                priorityQueue.add(new Pair<>(vc,file));
             }
         }
 
@@ -318,15 +319,19 @@ public class CatVariants extends CommandLineProgram {
         }
     }
 
-    private static class PositionComparator implements Comparator<Pair<Integer,File>> {
+    private static class PositionComparator implements Comparator<Pair<VariantContext,File>> {
+    	
+    	VariantContextComparator comp;
+    	
+    	public PositionComparator(final SAMSequenceDictionary dict){
+    		comp = new VariantContextComparator(dict);
+    	}
 
         @Override
-        public int compare(Pair<Integer,File> p1, Pair<Integer,File> p2) {
-            int startPositionP1 = p1.getFirst();
-            int startPositionP2 = p2.getFirst();
-            if (startPositionP1  == startPositionP2)
-                return 0;
-            return startPositionP1 < startPositionP2 ? -1 : 1 ;
+        public int compare(final Pair<VariantContext,File> p1, final Pair<VariantContext,File> p2) {
+            final VariantContext startPositionP1 = p1.getFirst();
+            final VariantContext startPositionP2 = p2.getFirst();
+            return comp.compare(startPositionP1, startPositionP2);
         }
     }
 }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
index 69ae7a472..0e9c80451 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
@@ -57,6 +57,8 @@ public class CatVariantsIntegrationTest {
     private final File CatVariantsVcf2 = new File(CatVariantsDir, "CatVariantsTest2.vcf");
     private final File CatVariantsBcf1 = new File(CatVariantsDir, "CatVariantsTest1.bcf");
     private final File CatVariantsBcf2 = new File(CatVariantsDir, "CatVariantsTest2.bcf");
+    private final File CatVariantsVcf3 = new File(CatVariantsDir, "CatVariantsTest3.vcf");
+    private final File CatVariantsVcf4 = new File(CatVariantsDir, "CatVariantsTest4.vcf");
 
     private class CatVariantsTestProvider extends BaseTest.TestDataProvider {
         private final File file1;
@@ -126,6 +128,27 @@ public class CatVariantsIntegrationTest {
         }
     }
 
+    @DataProvider(name = "SortOrderTest")
+    public Object[][] makeSortOrderTestProvider() {
+        new CatVariantsTestProvider(CatVariantsVcf3, CatVariantsVcf4, BaseTest.createTempFile("CatVariantsSortOrderTest", ".vcf"), "7bfe34c78b9f1b56a28cc33262cdfd97");
+
+        return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
+    }
+
+    @Test(dataProvider = "SortOrderTest")
+    public void testSortOrder(final CatVariantsTestProvider cfg) throws IOException {
+
+        ProcessController pc = ProcessController.getThreadLocal();
+        ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cfg.getCmdLine()));
+        pc.execAndCheck(ps);
+
+        MD5DB.MD5Match result = md5db.testFileMD5("testSortOrder", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
+        if(result.failed) {
+            final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
+            Assert.fail(failure.toString());
+        }
+    }
+
     @DataProvider(name = "MismatchedExtensionsTest")
     public Object[][] makeMismatchedExtensionsTestProvider() {
         return new Object[][]{