diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index e3f9b8ee3..5726eeed9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -27,15 +27,12 @@ package org.broadinstitute.sting.gatk.walkers.diffengine;
 import org.apache.log4j.Logger;
 import org.broad.tribble.AbstractFeatureReader;
 import org.broad.tribble.FeatureReader;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
-import java.util.Arrays;
 import java.util.Iterator;
 import java.util.Map;
 
@@ -69,7 +66,7 @@ public class VCFDiffableReader implements DiffableReader {
 
             FeatureReader<VariantContext> reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), vcfCodec, false);
             VCFHeader header = (VCFHeader)reader.getHeader();
-            for ( VCFHeaderLine headerLine : header.getMetaData() ) {
+            for ( VCFHeaderLine headerLine : header.getMetaDataInInputOrder() ) {
                 String key = headerLine.getKey();
                 if ( headerLine instanceof VCFIDHeaderLine)
                     key += "_" + ((VCFIDHeaderLine) headerLine).getID();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
index 9a22e8cf6..5bbc6dacc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
@@ -102,7 +102,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
         if (useSingleSample != null) { // only want to output context for one sample
             Set<String> singSampSet = new TreeSet<String>();
             singSampSet.add(useSingleSample);
-            header = new VCFHeader(header.getMetaData(), singSampSet);
+            header = new VCFHeader(header.getMetaDataInSortedOrder(), singSampSet);
         }
 
         innerWriter.writeHeader(header);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index 485f3394b..43816b0fa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -63,7 +63,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaData() : null, samples);
+        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : null, samples);
         writer.writeHeader(vcfHeader);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 484400025..c1755aa00 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -92,7 +92,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
-        Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaData();
+        Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
         baseWriter.writeHeader(new VCFHeader(headerLines, samples));
 
         writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 21965afcd..60d41abd5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -95,7 +95,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
         Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
         if ( vcfHeaders.containsKey(trackName) )
-            metaData.addAll(vcfHeaders.get(trackName).getMetaData());
+            metaData.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder());
         if ( RECORD_ORIGINAL_LOCATION ) {
             metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record"));
             metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record"));
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
index 0503e417a..18b4d0b6c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
@@ -385,10 +385,14 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
         if ( value == null )
             builder.unfiltered();
         else {
-            if ( value instanceof Integer )
+            if ( value instanceof Integer ) {
                 // fast path for single integer result
-                builder.filter(getDictionaryString((Integer)value));
-            else {
+                final String filterString = getDictionaryString((Integer)value);
+                if ( VCFConstants.PASSES_FILTERS_v4.equals(filterString))
+                    builder.passFilters();
+                else
+                    builder.filter(filterString);
+            } else {
                 for ( final int offset : (List<Integer>)value )
                     builder.filter(getDictionaryString(offset));
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
index 21deb4158..143ab52df 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
@@ -26,10 +26,7 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFIDHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
@@ -84,8 +81,8 @@ public final class BCF2Utils {
 
         boolean sawPASS = false;
         // set up the strings dictionary
-        for ( VCFHeaderLine line : header.getMetaData() ) {
-            if ( line instanceof VCFIDHeaderLine) {
+        for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
+            if ( line instanceof VCFIDHeaderLine && ! (line instanceof VCFContigHeaderLine) ) {
                 final VCFIDHeaderLine idLine = (VCFIDHeaderLine)line;
                 if ( ! seen.contains(idLine.getID())) {
                     sawPASS = sawPASS || idLine.getID().equals(VCFConstants.PASSES_FILTERS_v4);
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 5ad939e76..b3420514b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -115,7 +115,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
     protected VCFHeader parseHeaderFromLines( final List<String> headerStrings, final VCFHeaderVersion version ) {
         this.version = version;
 
-        Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
+        Set<VCFHeaderLine> metaData = new LinkedHashSet<VCFHeaderLine>();
         Set<String> sampleNames = new LinkedHashSet<String>();
         int contigCounter = 0;
         // iterate over all the passed in strings
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
index 296be7873..7a9329583 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
@@ -52,7 +52,7 @@ public class VCFHeader {
     }
 
     // the associated meta data
-    private final Set<VCFHeaderLine> mMetaData = new TreeSet<VCFHeaderLine>();
+    private final Set<VCFHeaderLine> mMetaData = new LinkedHashSet<VCFHeaderLine>();
     private final Map<String, VCFInfoHeaderLine> mInfoMetaData = new HashMap<String, VCFInfoHeaderLine>();
     private final Map<String, VCFFormatHeaderLine> mFormatMetaData = new HashMap<String, VCFFormatHeaderLine>();
     private final Map<String, VCFFilterHeaderLine> mFilterMetaData = new HashMap<String, VCFFilterHeaderLine>();
@@ -230,14 +230,22 @@ public class VCFHeader {
     }
 
     /**
-     * get the meta data, associated with this header
+     * get the meta data, associated with this header, in sorted order
      *
      * @return a set of the meta data
      */
-    public Set<VCFHeaderLine> getMetaData() {
-        Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
+    public Set<VCFHeaderLine> getMetaDataInInputOrder() {
+        return makeGetMetaDataSet(mMetaData);
+    }
+
+    public Set<VCFHeaderLine> getMetaDataInSortedOrder() {
+        return makeGetMetaDataSet(new TreeSet<VCFHeaderLine>(mMetaData));
+    }
+
+    private static Set<VCFHeaderLine> makeGetMetaDataSet(final Set<VCFHeaderLine> headerLinesInSomeOrder) {
+        final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
         lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_1.getFormatString(), VCFHeaderVersion.VCF4_1.getVersionString()));
-        lines.addAll(mMetaData);
+        lines.addAll(headerLinesInSomeOrder);
         return Collections.unmodifiableSet(lines);
     }
 
@@ -247,7 +255,7 @@ public class VCFHeader {
      * @return
      */
     public VCFHeaderLine getMetaDataLine(final String key) {
-        for (final VCFHeaderLine line: getMetaData()) {
+        for (final VCFHeaderLine line: mMetaData) {
             if ( line.getKey().equals(key) )
                 return line;
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
index 40d22f46f..b2e8cc100 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.utils.codecs.vcf;
 
 import com.google.java.contract.Ensures;
-import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -60,8 +59,8 @@ public class VCFStandardHeaderLines {
     @Requires("header != null")
     @Ensures("result != null")
     public static VCFHeader repairStandardHeaderLines(final VCFHeader header) {
-        final Set<VCFHeaderLine> newLines = new LinkedHashSet<VCFHeaderLine>(header.getMetaData().size());
-        for ( VCFHeaderLine line : header.getMetaData() ) {
+        final Set<VCFHeaderLine> newLines = new LinkedHashSet<VCFHeaderLine>(header.getMetaDataInInputOrder().size());
+        for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
             if ( line instanceof VCFFormatHeaderLine ) {
                 line = formatStandards.repair((VCFFormatHeaderLine) line);
             } else if ( line instanceof VCFInfoHeaderLine) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index dc7bcd926..f80b0eae4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -25,8 +25,6 @@
 
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
@@ -34,7 +32,6 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
@@ -129,7 +126,7 @@ public class VCFUtils {
             if ( source.getRecordType().equals(VariantContext.class)) {
                 VCFHeader header = (VCFHeader)source.getHeader();
                 if ( header != null )
-                    fields.addAll(header.getMetaData());
+                    fields.addAll(header.getMetaDataInSortedOrder());
             }
         }
 
@@ -160,7 +157,7 @@ public class VCFUtils {
         // todo -- needs to remove all version headers from sources and add its own VCF version line
         for ( VCFHeader source : headers ) {
             //System.out.printf("Merging in header %s%n", source);
-            for ( VCFHeaderLine line : source.getMetaData()) {
+            for ( VCFHeaderLine line : source.getMetaDataInSortedOrder()) {
 
                 String key = line.getKey();
                 if ( line instanceof VCFIDHeaderLine )
@@ -250,7 +247,7 @@ public class VCFUtils {
      * @param refDict the SAM formatted reference sequence dictionary
      */
     public final static VCFHeader withUpdatedContigs(final VCFHeader oldHeader, final File referenceFile, final SAMSequenceDictionary refDict) {
-        return new VCFHeader(withUpdatedContigsAsLines(oldHeader.getMetaData(), referenceFile, refDict), oldHeader.getGenotypeSamples());
+        return new VCFHeader(withUpdatedContigsAsLines(oldHeader.getMetaDataInInputOrder(), referenceFile, refDict), oldHeader.getGenotypeSamples());
     }
 
     public final static Set<VCFHeaderLine> withUpdatedContigsAsLines(final Set<VCFHeaderLine> oldLines, final File referenceFile, final SAMSequenceDictionary refDict) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
index 0590329c4..f2375f6f9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
@@ -260,6 +260,7 @@ public class VariantContextBuilder {
         return this;
     }
 
+    @Requires({"filter != null", "!filter.equals(\"PASS\")"})
     public VariantContextBuilder filter(final String filter) {
         if ( this.filters == null ) this.filters = new LinkedHashSet<String>(1);
         this.filters.add(filter);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
index 7d9a18d14..45610bbf9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
@@ -109,7 +109,10 @@ class BCF2Writer extends IndexingVariantContextWriter {
     // --------------------------------------------------------------------------------
 
     @Override
-    public void writeHeader(final VCFHeader header) {
+    public void writeHeader(VCFHeader header) {
+        // make sure the header is sorted correctly
+        header = new VCFHeader(header.getMetaDataInSortedOrder(), header.getGenotypeSamples());
+
         // create the config offsets map
         if ( header.getContigLines().isEmpty() ) {
             if ( ALLOW_MISSING_CONTIG_LINES ) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
index 8ccb79744..4548e026e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
@@ -87,13 +87,13 @@ class VCFWriter extends IndexingVariantContextWriter {
                                         final boolean doNotWriteGenotypes,
                                         final String versionLine,
                                         final String streamNameForError) {
-        header = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header;
+        header = doNotWriteGenotypes ? new VCFHeader(header.getMetaDataInSortedOrder()) : header;
         
         try {
             // the file format field needs to be written first
             writer.write(versionLine + "\n");
 
-            for ( VCFHeaderLine line : header.getMetaData() ) {
+            for ( VCFHeaderLine line : header.getMetaDataInSortedOrder() ) {
                 if ( VCFHeaderVersion.isFormatString(line.getKey()) )
                     continue;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
index b8d6f2d1d..62d584ef6 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.codecs.vcf;
 
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
@@ -26,7 +25,7 @@ public class VCFHeaderUnitTest extends BaseTest {
     private VCFHeader createHeader(String headerStr) {
         VCFCodec codec = new VCFCodec();
         VCFHeader header = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
-        Assert.assertEquals(header.getMetaData().size(), VCF4headerStringCount);
+        Assert.assertEquals(header.getMetaDataInInputOrder().size(), VCF4headerStringCount);
         return header;
     }
 
@@ -98,7 +97,7 @@ public class VCFHeaderUnitTest extends BaseTest {
         } catch (IOException e) {
             Assert.fail("Unable to make a temp file!");
         }
-        for (VCFHeaderLine line : header.getMetaData())
+        for (VCFHeaderLine line : header.getMetaDataInSortedOrder())
             pw.println(line);
         pw.close();
         Assert.assertEquals(md5SumFile(myTempFile), md5sum);
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
index 1e3c799fe..b271d8c84 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
@@ -59,7 +59,7 @@ public class VCFIntegrationTest extends WalkerTest {
         executeTest("Test writing samtools WEx BCF example", spec1);
     }
 
-    @Test(enabled = false) // TODO disabled because current BCF2 is 1 based
+    @Test(enabled = false)
     public void testReadingSamtoolsWExBCFExample() {
         String testVCF = privateTestDir + "ex2.bcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
index 94ed2ce5f..ca4cdf306 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
@@ -106,7 +106,7 @@ public class VariantContextTestProvider {
             for ( final VariantContext vc : vcs )
                 if ( vc.hasGenotypes() )
                     samples.addAll(vc.getSampleNames());
-            this.header = samples.isEmpty() ? header : new VCFHeader(header.getMetaData(), samples);
+            this.header = samples.isEmpty() ? header : new VCFHeader(header.getMetaDataInSortedOrder(), samples);
             this.vcs = vcs;
         }
 
@@ -885,12 +885,12 @@ public class VariantContextTestProvider {
     }
 
     public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
-        Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size(), "No VCF header lines");
+        Assert.assertEquals(actual.getMetaDataInSortedOrder().size(), expected.getMetaDataInSortedOrder().size(), "No VCF header lines");
 
         // for some reason set.equals() is returning false but all paired elements are .equals().  Perhaps compare to is busted?
-        //Assert.assertEquals(actual.getMetaData(), expected.getMetaData());
-        final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaData());
-        final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaData());
+        //Assert.assertEquals(actual.getMetaDataInInputOrder(), expected.getMetaDataInInputOrder());
+        final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaDataInSortedOrder());
+        final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaDataInSortedOrder());
         for ( int i = 0; i < actualLines.size(); i++ ) {
             Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
         }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
index d4e489420..a7fff4559 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
@@ -39,9 +39,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VCFWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -166,7 +163,7 @@ public class VCFWriterUnitTest extends BaseTest {
             Assert.assertEquals(VCFHeader.HEADER_FIELDS.values()[index], field);
             index++;
         }
-        Assert.assertEquals(header.getMetaData().size(), metaData.size());
+        Assert.assertEquals(header.getMetaDataInSortedOrder().size(), metaData.size());
         index = 0;
         for (String key : header.getGenotypeSamples()) {
             Assert.assertTrue(additionalColumns.contains(key));