diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 3d3299053..4738f01c7 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -1204,9 +1204,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     /**
      * Is writing to an output GVCF file?
      *
-     * @return true if the VCF output file has a .g.vcf extension
+     * @return true if the VCF output file has a .g.vcf or .g.vcf.gz extension
      */
     private boolean isGVCF() {
-            return ((VariantContextWriterStub) vcfWriter).getOutputFile().getName().endsWith("." + GATKVCFUtils.GVCF_EXT);
+        String fileName = ((VariantContextWriterStub) vcfWriter).getOutputFile().getName();
+        return ( fileName.endsWith("." + GATKVCFUtils.GVCF_EXT) || fileName.endsWith("." + GATKVCFUtils.GVCF_GZ_EXT) );
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index 42c8c6285..6f5634b56 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -224,6 +224,18 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         executeTest("testGVCFIndexNoThrow", spec);
     }
 
+    /**
+     * Test HaplotypeCaller to ensure it does not throw an exception when a .g.vcf.gz output file is specified and the indexing arguments are omitted
+     */
+    @Test()
+    public void testGVCFGzIndexNoThrow() {
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000000-17000100");
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine  + " -o %s", Arrays.asList(GATKVCFUtils.GVCF_GZ_EXT), Arrays.asList(""));
+        spec.disableShadowBCF();
+        executeTest("testGVCFIndexNoThrow", spec);
+    }
+
     @Test()
     public void testWrongParameterGVCFIndexException() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
index da3763f1a..4d05d824e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
@@ -69,8 +69,9 @@ public class GATKVCFUtils {
     public final static GATKVCFIndexType DEFAULT_GVCF_INDEX_TYPE = GATKVCFIndexType.LINEAR;
     public final static Integer DEFAULT_GVCF_INDEX_PARAMETER = 128000;
 
-    // GVCF file extension
+    // GVCF file extensions
     public final static String GVCF_EXT = "g.vcf";
+    public final static String GVCF_GZ_EXT = "g.vcf.gz";
 
     // Message for using the deprecated --variant_index_type or --variant_index_parameter arguments.
     public final static String DEPRECATED_INDEX_ARGS_MSG = "Naming your output file using the .g.vcf extension will automatically set the appropriate values " +
@@ -389,7 +390,7 @@ public class GATKVCFUtils {
             indexType = variantIndexType;
             indexParameter = variantIndexParameter;
             logger.warn(DEPRECATED_INDEX_ARGS_MSG);
-        } else if (outputFile.getName().endsWith("."  + GVCF_EXT)) {
+        } else if (outputFile.getName().endsWith("."  + GVCF_EXT) || outputFile.getName().endsWith("."  + GVCF_GZ_EXT)) {
             indexType = DEFAULT_GVCF_INDEX_TYPE;
             indexParameter = DEFAULT_GVCF_INDEX_PARAMETER;
         }
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 18a2d6c12..69ae7a472 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
@@ -246,4 +246,20 @@ public class CatVariantsIntegrationTest {
         ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
         pc.execAndCheck(ps);
     }
+
+    @Test()
+    public void testCatVariantsGVCFGzIndexCreation() throws IOException{
+
+        String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s -out %s",
+                StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
+                CatVariants.class.getCanonicalName(),
+                BaseTest.b37KGReference,
+                CatVariantsVcf1,
+                CatVariantsVcf2,
+                BaseTest.createTempFile("CatVariantsGVCFIndexCreationTest", "." + GATKVCFUtils.GVCF_GZ_EXT));
+
+        ProcessController pc = ProcessController.getThreadLocal();
+        ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
+        pc.execAndCheck(ps);
+    }
 }
\ No newline at end of file