diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java
new file mode 100644
index 000000000..8568c1aab
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java
@@ -0,0 +1,252 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.gvcf;
+
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * GATK binary VCF record
+ *
+ * @author Your Name
+ * @since Date created
+ */
+public class GVCF {
+    private final static int RECORD_TERMINATOR = 123456789;
+    private int chromOffset;
+    private int start, stop;
+    private String id;
+    private List<Allele> alleleMap;
+    private int alleleOffsets[];
+    private float qual;
+    private byte refPad;
+    private String info;
+    private int filterOffset;
+
+    private List<GVCFGenotype> genotypes = Collections.emptyList();
+
+    public GVCF(final GVCFHeaderBuilder gvcfHeaderBuilder, final VariantContext vc, boolean skipGenotypes) {
+        chromOffset = gvcfHeaderBuilder.encodeString(vc.getChr());
+        start = vc.getStart();
+        stop = vc.getEnd();
+        refPad = vc.hasReferenceBaseForIndel() ? vc.getReferenceBaseForIndel() : 0;
+        id = vc.getID();
+
+        // encode alleles
+        alleleMap = new ArrayList<Allele>(vc.getNAlleles());
+        alleleOffsets = new int[vc.getNAlleles()];
+        alleleMap.add(vc.getReference());
+        alleleOffsets[0] = gvcfHeaderBuilder.encodeAllele(vc.getReference());
+        for ( int i = 0; i < vc.getAlternateAlleles().size(); i++ ) {
+            alleleMap.add(vc.getAlternateAllele(i));
+            alleleOffsets[i+1] = gvcfHeaderBuilder.encodeAllele(vc.getAlternateAllele(i));
+        }
+
+        qual = (float)vc.getNegLog10PError(); //qualToByte(vc.getPhredScaledQual());
+        info = infoFieldString(vc, gvcfHeaderBuilder);
+        filterOffset = gvcfHeaderBuilder.encodeString(StandardVCFWriter.getFilterString(vc));
+
+        if ( ! skipGenotypes ) {
+            genotypes = encodeGenotypes(gvcfHeaderBuilder, vc);
+        }
+    }
+
+    public GVCF(DataInputStream inputStream, boolean skipGenotypes) throws IOException {
+        chromOffset = inputStream.readInt();
+        start = inputStream.readInt();
+        stop = inputStream.readInt();
+        id = inputStream.readUTF();
+        refPad = inputStream.readByte();
+        alleleOffsets = readIntArray(inputStream);
+        qual = inputStream.readFloat();
+        info = inputStream.readUTF();
+        filterOffset = inputStream.readInt();
+
+        int nGenotypes = inputStream.readInt();
+        int sizeOfGenotypes = inputStream.readInt();
+        if ( skipGenotypes ) {
+            genotypes = Collections.emptyList();
+            inputStream.skipBytes(sizeOfGenotypes);
+        } else {
+            genotypes = new ArrayList<GVCFGenotype>(nGenotypes);
+            for ( int i = 0; i < nGenotypes; i++ )
+                genotypes.add(new GVCFGenotype(this, inputStream));
+        }
+
+        int recordDone = inputStream.readInt();
+        if ( recordDone != RECORD_TERMINATOR )
+            throw new UserException.MalformedFile("Record not terminated by RECORD_TERMINATOR key");
+    }
+
+    public VariantContext decode(final String source, final GVCFHeader header) {
+        final String contig = header.getString(chromOffset);
+        alleleMap = header.getAlleles(alleleOffsets);
+        double negLog10PError = qual; // QualityUtils.qualToErrorProb(qual);
+        Set<String> filters = header.getFilters(filterOffset);
+        Map<String, Object> attributes = new HashMap<String, Object>();
+        attributes.put("INFO", info);
+        Byte refPadByte = refPad == 0 ? null : refPad;
+        Map<String, Genotype> genotypes = decodeGenotypes(header);
+
+        return new VariantContext(source, contig, start, stop, alleleMap, genotypes, negLog10PError, filters, attributes, refPadByte);
+    }
+
+    private Map<String, Genotype> decodeGenotypes(final GVCFHeader header) {
+        if ( genotypes.isEmpty() )
+            return VariantContext.NO_GENOTYPES;
+        else {
+            Map<String, Genotype> map = new TreeMap<String, Genotype>();
+
+            for ( int i = 0; i < genotypes.size(); i++ ) {
+                final String sampleName = header.getSample(i);
+                final Genotype g = genotypes.get(i).decode(sampleName, header, this, alleleMap);
+                map.put(sampleName, g);
+            }
+
+            return map;
+        }
+    }
+
+    private List<GVCFGenotype> encodeGenotypes(final GVCFHeaderBuilder gvcfHeaderBuilder, final VariantContext vc) {
+        int nGenotypes = vc.getNSamples();
+        if ( nGenotypes > 0 ) {
+            List<GVCFGenotype> genotypes = new ArrayList<GVCFGenotype>(nGenotypes);
+            for ( int i = 0; i < nGenotypes; i++ ) genotypes.add(null);
+
+            for ( Genotype g : vc.getGenotypes().values() ) {
+                int i = gvcfHeaderBuilder.encodeSample(g.getSampleName());
+                genotypes.set(i, new GVCFGenotype(gvcfHeaderBuilder, alleleMap, g));
+            }
+
+            return genotypes;
+        } else {
+            return Collections.emptyList();
+        }
+    }
+
+    public int getNAlleles() { return alleleOffsets.length; }
+
+    public int write(DataOutputStream outputStream) throws IOException {
+        int startSize = outputStream.size();
+        outputStream.writeInt(chromOffset);
+        outputStream.writeInt(start);
+        outputStream.writeInt(stop);
+        outputStream.writeUTF(id);
+        outputStream.writeByte(refPad);
+        writeIntArray(alleleOffsets, outputStream, true);
+        outputStream.writeFloat(qual);
+        outputStream.writeUTF(info);
+        outputStream.writeInt(filterOffset);
+
+        int nGenotypes = genotypes.size();
+        int expectedSizeOfGenotypes = nGenotypes == 0 ? 0 : genotypes.get(0).sizeInBytes() * nGenotypes;
+        outputStream.writeInt(nGenotypes);
+        outputStream.writeInt(expectedSizeOfGenotypes);
+        int obsSizeOfGenotypes = 0;
+        for ( GVCFGenotype g : genotypes )
+            obsSizeOfGenotypes += g.write(outputStream);
+        if ( obsSizeOfGenotypes != expectedSizeOfGenotypes )
+            throw new RuntimeException("Expect and observed genotype sizes disagree! expect = " + expectedSizeOfGenotypes + " obs =" + obsSizeOfGenotypes);
+
+        outputStream.writeInt(RECORD_TERMINATOR);
+        return outputStream.size() - startSize;
+    }
+
+    private final String infoFieldString(VariantContext vc, final GVCFHeaderBuilder gvcfHeaderBuilder) {
+        StringBuilder s = new StringBuilder();
+
+        boolean first = true;
+        for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
+            String key = field.getKey();
+            if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
+                continue;
+            int stringIndex = gvcfHeaderBuilder.encodeString(key);
+            String outputValue = StandardVCFWriter.formatVCFField(field.getValue());
+            if ( outputValue != null ) {
+                if ( ! first ) s.append(";");
+                s.append(stringIndex).append("=").append(outputValue);
+                first = false;
+            }
+        }
+
+        return s.toString();
+    }
+
+    private final static int BUFFER_SIZE = 1048576; // 2**20
+    public static DataOutputStream createOutputStream(final File file) throws FileNotFoundException {
+        return new DataOutputStream(new BufferedOutputStream(new FileOutputStream(file), BUFFER_SIZE));
+    }
+
+    public static DataInputStream createInputStream(final File file) throws FileNotFoundException {
+        return new DataInputStream(new BufferedInputStream(new FileInputStream(file), BUFFER_SIZE));
+    }
+
+    protected final static int[] readIntArray(final DataInputStream inputStream) throws IOException {
+        return readIntArray(inputStream, inputStream.readInt());
+    }
+
+    protected final static int[] readIntArray(final DataInputStream inputStream, int size) throws IOException {
+        int[] array = new int[size];
+        for ( int i = 0; i < array.length; i++ )
+            array[i] = inputStream.readInt();
+        return array;
+    }
+
+    protected final static void writeIntArray(int[] array, final DataOutputStream outputStream, boolean writeSize) throws IOException {
+        if ( writeSize ) outputStream.writeInt(array.length);
+        for ( int i : array )
+            outputStream.writeInt(i);
+    }
+
+    protected final static byte[] readByteArray(final DataInputStream inputStream) throws IOException {
+        return readByteArray(inputStream, inputStream.readInt());
+    }
+
+    protected final static byte[] readByteArray(final DataInputStream inputStream, int size) throws IOException {
+        byte[] array = new byte[size];
+        for ( int i = 0; i < array.length; i++ )
+            array[i] = inputStream.readByte();
+        return array;
+    }
+
+    protected final static void writeByteArray(byte[] array, final DataOutputStream outputStream, boolean writeSize) throws IOException {
+        if ( writeSize ) outputStream.writeInt(array.length);
+        for ( byte i : array )
+            outputStream.writeByte(i);
+    }
+
+    protected final static byte qualToByte(double phredScaledQual) {
+        return (byte)Math.round(Math.min(phredScaledQual, 255));
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java
new file mode 100644
index 000000000..2ef6d9b3a
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java
@@ -0,0 +1,147 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.gvcf;
+
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
+import java.util.*;
+
+/**
+ * GATK binary VCF record
+ *
+ * @author Your Name
+ * @since Date created
+ */
+public class GVCFGenotype {
+    private byte gq;
+    private int gt;
+    private int dp;
+    private int ad[];
+    private byte[] pl;
+
+    // todo -- what to do about phasing?  Perhaps we shouldn't support it
+    // todo -- is the FL field generic or just a flag?  Should we even support per sample filtering?
+
+    public GVCFGenotype(final GVCFHeaderBuilder gvcfHeaderBuilder, final List<Allele> allAlleles, Genotype genotype) {
+        gq = GVCF.qualToByte(genotype.getPhredScaledQual());
+        gt = encodeAlleles(genotype.getAlleles(), allAlleles);
+
+        dp = genotype.getAttributeAsInt("DP", 0);
+
+        int nAlleles = allAlleles.size();
+        ad = new int[nAlleles];
+
+        int npls = nAllelesToNPls(nAlleles);
+        pl = new byte[npls];
+    }
+
+    private int nAllelesToNPls( int nAlleles ) {
+        return nAlleles*(nAlleles+1) / 2;
+    }
+
+    public GVCFGenotype(GVCF gvcf, DataInputStream inputStream) throws IOException {
+        int gqInt = inputStream.readUnsignedByte();
+        gq = (byte)gqInt;
+        gt = inputStream.readInt();
+        dp = inputStream.readInt();
+        ad = GVCF.readIntArray(inputStream, gvcf.getNAlleles());
+        pl = GVCF.readByteArray(inputStream, nAllelesToNPls(gvcf.getNAlleles()));
+    }
+
+    // 2 alleles => 1 + 8 + 8 + 3 => 20
+    protected int sizeInBytes() {
+        return 1 // gq
+                + 4 * 2 // gt + dp
+                + 4 * ad.length // ad
+                + 1 * pl.length; // pl
+    }
+
+    public Genotype decode(final String sampleName, final GVCFHeader header, GVCF gvcf, List<Allele> alleleIndex) {
+        final List<Allele> alleles = decodeAlleles(gt, alleleIndex);
+        final double negLog10PError = gq / 10.0;
+        final Set<String> filters = Collections.emptySet();
+        final Map<String, Object> attributes = new HashMap<String, Object>();
+        attributes.put("DP", dp);
+        attributes.put("AD", ad);
+        attributes.put("PL", pl);
+
+        return new Genotype(sampleName, alleles, negLog10PError, filters, attributes, false);
+    }
+
+    private static int encodeAlleles(List<Allele> gtList, List<Allele> allAlleles) {
+        final int nAlleles = gtList.size();
+        if ( nAlleles  > 4 )
+            throw new IllegalArgumentException("encodeAlleles doesn't support more than 4 alt alleles, but I saw " + gtList);
+
+        int gtInt = 0;
+        for ( int i = 0; i < nAlleles ; i++ ) {
+            final int bitOffset = i * 8;
+            final int allelei = getAlleleIndex(gtList.get(i), allAlleles);
+            final int gti = (allelei + 1) << bitOffset;
+            gtInt = gtInt | gti;
+        }
+
+        return gtInt;
+    }
+
+    private static int getAlleleIndex(Allele q, List<Allele> allAlleles) {
+        if ( q.isNoCall() )
+            return 254;
+        for ( int i = 0; i < allAlleles.size(); i++ )
+            if ( q.equals(allAlleles.get(i)) )
+                return i;
+        throw new IllegalStateException("getAlleleIndex passed allele not in map! allele " + q + " allAlleles " + allAlleles);
+    }
+
+    private static List<Allele> decodeAlleles(int gtInt, List<Allele> alleleIndex) {
+        List<Allele> alleles = new ArrayList<Allele>(4);
+
+        for ( int i = 0; i < 32; i += 8 ) {
+            final int gi = (gtInt & (0x000000FF << i)) >> i;
+            if ( gi != 0 ) {
+                final int allelei = gi - 1;
+                alleles.add( allelei == 254 ? Allele.NO_CALL : alleleIndex.get(allelei) );
+            } else {
+                break;
+            }
+        }
+
+        return alleles;
+    }
+
+    public int write(DataOutputStream outputStream) throws IOException {
+        int startSize = outputStream.size();
+        outputStream.writeByte(gq);
+        outputStream.writeInt(gt);
+        outputStream.writeInt(dp);
+        GVCF.writeIntArray(ad, outputStream, false);
+        GVCF.writeByteArray(pl, outputStream, false);
+        return outputStream.size() - startSize;
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java
new file mode 100644
index 000000000..c52c975bd
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java
@@ -0,0 +1,180 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.gvcf;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
+import java.util.*;
+
+/**
+ * [Short one sentence description of this walker]
+ * <p/>
+ * <p>
+ * [Functionality of this walker]
+ * </p>
+ * <p/>
+ * <h2>Input</h2>
+ * <p>
+ * [Input description]
+ * </p>
+ * <p/>
+ * <h2>Output</h2>
+ * <p>
+ * [Output description]
+ * </p>
+ * <p/>
+ * <h2>Examples</h2>
+ * <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *  </pre>
+ *
+ * @author Your Name
+ * @since Date created
+ */
+public class GVCFHeader {
+    final protected static Logger logger = Logger.getLogger(GVCFHeader.class);
+
+    private static byte[] MAGIC_HEADER = "GVCF0.1\1".getBytes();
+    final List<Allele> alleles;
+    final List<String> strings;
+    final List<String> samples;
+    final List<Set<String>> filters;
+
+    public GVCFHeader(final Map<Allele, Integer> allelesIn, final Map<String, Integer> stringIn, final Map<String, Integer> samplesIn) {
+        this.alleles = linearize(allelesIn);
+        this.strings = linearize(stringIn);
+        this.samples = linearize(samplesIn);
+        this.filters = null; // not used with this constructor
+    }
+
+    public GVCFHeader(DataInputStream inputStream) throws IOException {
+        byte[] headerTest = new byte[MAGIC_HEADER.length];
+        inputStream.read(headerTest);
+        if ( ! Arrays.equals(headerTest, MAGIC_HEADER) ) {
+            throw new UserException("Could not read GVCF file.  MAGIC_HEADER missing.  Saw " + headerTest);
+        } else {
+            alleles = stringsToAlleles(readStrings(inputStream));
+            strings = readStrings(inputStream);
+            samples = readStrings(inputStream);
+            logger.info(String.format("Allele map of %d elements", alleles.size()));
+            logger.info(String.format("String map of %d elements", strings.size()));
+            logger.info(String.format("Sample map of %d elements", samples.size()));
+            filters = initializeFilterCache();
+        }
+    }
+
+    public int write(final DataOutputStream outputStream) throws IOException {
+        int startBytes = outputStream.size();
+        outputStream.write(MAGIC_HEADER);
+        write(outputStream, allelesToStrings(alleles));
+        write(outputStream, strings);
+        write(outputStream, samples);
+        return outputStream.size() - startBytes;
+    }
+
+    public void write(DataOutputStream outputStream, List<String> l) throws IOException {
+        outputStream.writeInt(l.size());
+        for ( String elt : l ) outputStream.writeUTF(elt);
+    }
+
+    private List<String> allelesToStrings(List<Allele> alleles) {
+        List<String> strings = new ArrayList<String>(alleles.size());
+        for ( Allele allele : alleles ) strings.add(allele.toString());
+        return strings;
+    }
+
+    private List<Set<String>> initializeFilterCache() {
+        // required to allow offset -> set lookup
+        List<Set<String>> l = new ArrayList<Set<String>>(strings.size());
+        for ( int i = 0; i < strings.size(); i++ ) l.add(null);
+        return l;
+    }
+
+    private static List<Allele> stringsToAlleles(final List<String> strings) {
+        final List<Allele> alleles = new ArrayList<Allele>(strings.size());
+        for ( String string : strings ) {
+            boolean isRef = string.endsWith("*");
+            if ( isRef ) string = string.substring(0, string.length() - 1);
+            alleles.add(Allele.create(string, isRef));
+        }
+        return alleles;
+    }
+
+    private static List<String> readStrings(final DataInputStream inputStream) throws IOException {
+        final int nStrings = inputStream.readInt();
+
+        final List<String> strings = new ArrayList<String>(nStrings);
+        for ( int i = 0; i < nStrings; i++ ) {
+            strings.add(inputStream.readUTF());
+        }
+
+        return strings;
+    }
+
+    private static <T> List<T> linearize(final Map<T, Integer> map) {
+        final ArrayList<T> l = new ArrayList<T>(map.size());
+        for ( int i = 0; i < map.size(); i++ ) l.add(null);
+        for ( final Map.Entry<T, Integer> elt : map.entrySet() )
+            l.set(elt.getValue(), elt.getKey());
+        return l;
+    }
+
+    public String getSample(final int offset) { return samples.get(offset); }
+    public String getString(final int offset) { return strings.get(offset); }
+    public Allele getAllele(final int offset) { return alleles.get(offset); }
+    public List<Allele> getAlleles(final int[] offsets) {
+        final List<Allele> alleles = new ArrayList<Allele>(offsets.length);
+        for ( int i : offsets ) alleles.add(getAllele(i));
+        return alleles;
+    }
+
+    public Set<String> getFilters(final int offset) {
+        Set<String> cached = filters.get(offset);
+
+        if ( cached != null )
+            return cached;
+        else {
+            final String filterString = getString(offset);
+            if ( filterString.equals(VCFConstants.UNFILTERED) )
+                return null; // UNFILTERED records are represented by null
+            else {
+                Set<String> set = VCFCodec.parseFilters(null, -1, filterString);
+                filters.set(offset, set); // remember the result
+                return set;
+            }
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java
new file mode 100644
index 000000000..2d045b8ea
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java
@@ -0,0 +1,80 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.gvcf;
+
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * [Short one sentence description of this walker]
+ * <p/>
+ * <p>
+ * [Functionality of this walker]
+ * </p>
+ * <p/>
+ * <h2>Input</h2>
+ * <p>
+ * [Input description]
+ * </p>
+ * <p/>
+ * <h2>Output</h2>
+ * <p>
+ * [Output description]
+ * </p>
+ * <p/>
+ * <h2>Examples</h2>
+ * <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *  </pre>
+ *
+ * @author Your Name
+ * @since Date created
+ */
+public class GVCFHeaderBuilder {
+    Map<Allele, Integer> alleles = new HashMap<Allele, Integer>();
+    Map<String, Integer> strings = new HashMap<String, Integer>();
+    Map<String, Integer> samples = new HashMap<String, Integer>();
+
+    public GVCFHeader createHeader() {
+        return new GVCFHeader(alleles, strings, samples);
+    }
+
+    public int encodeString(final String chr)    { return encode(strings, chr); }
+    public int encodeAllele(final Allele allele) { return encode(alleles, allele); }
+    public int encodeSample(final String sampleName) { return encode(samples, sampleName); }
+
+    private <T> int encode(Map<T, Integer> map, T key) {
+        Integer v = map.get(key);
+        if ( v == null ) {
+            v = map.size();
+            map.put(key, v);
+        }
+        return v;
+    }
+}