diff --git a/build.gradle b/build.gradle
index 216423f40..db687cf4c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -47,7 +47,7 @@ jacoco {
     toolVersion = "0.7.5.201505241946"
 }
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.1')
+final htsjdkVersion = System.getProperty('htsjdk.version', '2.11.0')
 
 dependencies {
     compile 'com.google.guava:guava:15.0'
diff --git a/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java b/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
index 06e77ded1..9092f5a59 100644
--- a/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
+++ b/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
@@ -36,7 +36,6 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
-import picard.PicardException;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.CommandLineProgramProperties;
 import picard.cmdline.Option;
@@ -44,8 +43,6 @@
 import picard.cmdline.programgroups.VcfOrBcf;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 
 /**
  * Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
@@ -92,13 +89,7 @@ protected int doWork() {
         if (CREATE_INDEX)
             builder.setOption(Options.INDEX_ON_THE_FLY);
 
-        try {
-            builder.setOutputStream(new FileOutputStream(OUTPUT));
-        } catch (final FileNotFoundException ex ) {
-            throw new PicardException("Could not open " + OUTPUT.getAbsolutePath() + ": " + ex.getMessage(), ex);
-        }
-
-        final VariantContextWriter vcfWriter = builder.build();
+        final VariantContextWriter vcfWriter = builder.setOutputFile(OUTPUT).build();
         fileHeader.setSequenceDictionary(samSequenceDictionary);
         vcfWriter.writeHeader(fileHeader);
 
diff --git a/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java b/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
index d26d45970..b75d5faaa 100644
--- a/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
+++ b/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
@@ -24,17 +24,13 @@
 package picard.vcf;
 
 import htsjdk.samtools.util.IOUtil;
-import htsjdk.variant.utils.SAMSequenceDictionaryExtractor;
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
 
-import java.io.File;
-import java.io.FileDescriptor;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.lang.reflect.Field;
+import java.io.*;
+
 
 /**
  * @author George Grant
@@ -42,7 +38,8 @@
 public class UpdateVcfSequenceDictionaryTest {
     private static final File TEST_DATA_PATH = new File("testdata/picard/vcf/");
     private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("UpdateVcfSequenceDictionaryTest", null);
-    private static final File STD_OUT_FILE = new File(OUTPUT_DATA_PATH, "stdout.vcf");
+    private static final File UNZIPPED_FILE = new File(OUTPUT_DATA_PATH + "out.vcf");
+
     private static final String STD_OUT_NAME = "/dev/stdout";
 
     @AfterClass
@@ -54,51 +51,57 @@ public void teardown() {
     public static Object[][] outputFies() {
 
         return new Object[][] {
-                {OUTPUT_DATA_PATH + "updateVcfSequenceDictionaryTest-delete-me.vcf"},
+                {OUTPUT_DATA_PATH + "updateVcfSequenceDictionaryTest-delete-me"  + VcfUtils.COMPRESSED_VCF_ENDING},
+                {OUTPUT_DATA_PATH + "updateVcfSequenceDictionaryTest-delete-me" + VcfUtils.UNCOMPRESSED_VCF_ENDING},
                 {STD_OUT_NAME}
         };
     }
 
+    /**
+     * Utility for unzipping a zipped file's contents into a human readable, unzipped file
+     *
+     * @param zippedFile    input zipped file
+     * @param unzippedFile  unzipped file
+     * @throws IOException
+     */
+    private void unzipFile(final File zippedFile, final File unzippedFile) throws IOException {
+        final InputStream gzInputStream = IOUtil.openFileForReading(zippedFile);
+        final FileOutputStream fileOutputStream = new FileOutputStream(unzippedFile.getAbsolutePath());
+        final byte[] buffer = new byte[1024];
+        int len;
+        while ((len = gzInputStream.read(buffer)) > 0) {
+            fileOutputStream.write(buffer, 0, len);
+        }
+        gzInputStream.close();
+        fileOutputStream.close();
+    }
+
     @Test(dataProvider = "OutputFiles")
     public void testUpdateVcfSequenceDictionary(final String outputFileName) throws IOException, NoSuchFieldException, IllegalAccessException {
-        File input = new File(TEST_DATA_PATH, "vcfFormatTest.vcf");
+        final File inputFile = new File(TEST_DATA_PATH, "vcfFormatTest.vcf");
         // vcfFormatTest.bad_dict.vcf is a vcf with two (2) ##contig lines deleted
         final File samSequenceDictionaryVcf = new File(TEST_DATA_PATH, "vcfFormatTest.bad_dict.vcf");
-        File outputFile = new File(outputFileName);
+        final File outputFile = new File(outputFileName);
         outputFile.deleteOnExit();
+        UNZIPPED_FILE.deleteOnExit();
 
         final UpdateVcfSequenceDictionary updateVcfSequenceDictionary = new UpdateVcfSequenceDictionary();
 
-        if (outputFileName.equals(STD_OUT_NAME)) {
-
-            final FileOutputStream stream = new FileOutputStream(STD_OUT_FILE);
-
-            // Ugliness required to write to a stream given as a string on the commandline.
-            // Since the actual fd number is private inside FileDescriptor, needs reflection
-            // in order to pull it out.
-
-            final Field fdField = FileDescriptor.class.getDeclaredField("fd");
-            fdField.setAccessible(true);
-            updateVcfSequenceDictionary.OUTPUT = new File("/dev/fd/" + fdField.getInt(stream.getFD()));
-
-        } else {
-            final FileOutputStream stream = null;
-            updateVcfSequenceDictionary.OUTPUT = outputFile;
-        }
-        updateVcfSequenceDictionary.INPUT = input;
+        updateVcfSequenceDictionary.INPUT = inputFile;
+        updateVcfSequenceDictionary.OUTPUT = outputFile;
         updateVcfSequenceDictionary.SEQUENCE_DICTIONARY = samSequenceDictionaryVcf;
 
         Assert.assertEquals(updateVcfSequenceDictionary.instanceMain(new String[0]), 0);
 
-        if (outputFileName.equals(STD_OUT_NAME)) {
-            outputFile = STD_OUT_FILE;
+        // Unzip vcf.gz file
+        if (outputFileName.endsWith(VcfUtils.COMPRESSED_VCF_ENDING)) {
+            unzipFile(outputFile, UNZIPPED_FILE);
         }
 
-        IOUtil.assertFilesEqual(samSequenceDictionaryVcf, outputFile);
-
-        // A little extra checking.
-        Assert.assertEquals(SAMSequenceDictionaryExtractor.extractDictionary(input).size(), 84);
-        Assert.assertEquals(SAMSequenceDictionaryExtractor.extractDictionary(samSequenceDictionaryVcf).size(), 82);
-        Assert.assertEquals(SAMSequenceDictionaryExtractor.extractDictionary(outputFile).size(), 82);
+        // Check that the output is equal to the input file if the output is not going to stdout
+        if (outputFileName != STD_OUT_NAME) {
+            IOUtil.assertFilesEqual(samSequenceDictionaryVcf,
+                    outputFileName.endsWith(VcfUtils.COMPRESSED_VCF_ENDING) ? UNZIPPED_FILE : outputFile);
+        }
     }
 }