diff --git a/java/src/org/broad/tribble/vcf/VCFFormatHeaderLine.java b/java/src/org/broad/tribble/vcf/VCFFormatHeaderLine.java
index ce8418d8e..989ed2c71 100755
--- a/java/src/org/broad/tribble/vcf/VCFFormatHeaderLine.java
+++ b/java/src/org/broad/tribble/vcf/VCFFormatHeaderLine.java
@@ -39,6 +39,11 @@ public class VCFFormatHeaderLine extends VCFHeaderLine {
     private String mDescription;
     private FORMAT_TYPE mType;
 
+    // info line numerical values are allowed to be unbounded (or unknown), which is
+    // marked with a dot (.)
+    public static int UNBOUNDED = -1;
+    public static String UNBOUNDED_ENCODING_VCF4 = ".";
+    public static String UNBOUNDED_ENCODING_VCF3 = "-1";
 
     /**
      * create a VCF format header line
@@ -67,7 +72,9 @@ public class VCFFormatHeaderLine extends VCFHeaderLine {
         super("FORMAT", "", version);
         Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
         mName = mapping.get("ID");
-        mCount = Integer.valueOf(mapping.get("Number"));
+        mCount = version == VCFHeaderVersion.VCF4_0 ?
+                        mapping.get("Number").equals(UNBOUNDED_ENCODING_VCF4) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")) :
+                        mapping.get("Number").equals(UNBOUNDED_ENCODING_VCF3) ? UNBOUNDED : Integer.valueOf(mapping.get("Number"));
         mType = FORMAT_TYPE.valueOf(mapping.get("Type"));
         mDescription = mapping.get("Description");
     }
@@ -78,7 +85,7 @@ public class VCFFormatHeaderLine extends VCFHeaderLine {
         else if (mVersion == VCFHeaderVersion.VCF4_0) {
             Map<String,Object> map = new LinkedHashMap<String,Object>();
             map.put("ID",mName);
-            map.put("Number",mCount);
+            map.put("Number",mCount == UNBOUNDED ? (mVersion == VCFHeaderVersion.VCF4_0 ? UNBOUNDED_ENCODING_VCF4 : UNBOUNDED_ENCODING_VCF3) : mCount);
             map.put("Type",mType);
             map.put("Description",mDescription);
             return "FORMAT=" + VCFHeaderLineTranslator.toValue(this.mVersion,map);
diff --git a/java/src/org/broad/tribble/vcf/VCFHeaderLineTranslator.java b/java/src/org/broad/tribble/vcf/VCFHeaderLineTranslator.java
index 84b5ca1c9..9aa7ae1dc 100644
--- a/java/src/org/broad/tribble/vcf/VCFHeaderLineTranslator.java
+++ b/java/src/org/broad/tribble/vcf/VCFHeaderLineTranslator.java
@@ -3,11 +3,7 @@ package org.broad.tribble.vcf;
 import java.util.*;
 
 /**
- * Created by IntelliJ IDEA.
- * User: aaron
- * Date: Jun 17, 2010
- * Time: 12:28:46 PM
- * To change this template use File | Settings | File Templates.
+ * A class for translating between vcf header versions
  */
 public class VCFHeaderLineTranslator {
     private static Map<VCFHeaderVersion,VCFLineParser> mapping;
diff --git a/java/src/org/broad/tribble/vcf/VCFInfoHeaderLine.java b/java/src/org/broad/tribble/vcf/VCFInfoHeaderLine.java
index 4d8d2c400..8a460879d 100755
--- a/java/src/org/broad/tribble/vcf/VCFInfoHeaderLine.java
+++ b/java/src/org/broad/tribble/vcf/VCFInfoHeaderLine.java
@@ -45,8 +45,9 @@ public class VCFInfoHeaderLine extends VCFHeaderLine {
 
     // info line numerical values are allowed to be unbounded (or unknown), which is
     // marked with a dot (.)
-    public static int UNBOUNDED = Integer.MIN_VALUE;
-    public static String UNBOUNDED_ENCODING = ".";
+    public static int UNBOUNDED = -1;
+    public static String UNBOUNDED_ENCODING_VCF4 = ".";
+    public static String UNBOUNDED_ENCODING_VCF3 = "-1";
 
     /**
      * create a VCF info header line
@@ -74,7 +75,9 @@ public class VCFInfoHeaderLine extends VCFHeaderLine {
         super("INFO", "", version);
         Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
         mName = mapping.get("ID");
-        mCount = mapping.get("Number").equals(UNBOUNDED_ENCODING) ? UNBOUNDED : Integer.valueOf(mapping.get("Number"));
+        mCount = version == VCFHeaderVersion.VCF4_0 ?
+                mapping.get("Number").equals(UNBOUNDED_ENCODING_VCF4) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")) :
+                mapping.get("Number").equals(UNBOUNDED_ENCODING_VCF3) ? UNBOUNDED : Integer.valueOf(mapping.get("Number"));
         mType = INFO_TYPE.valueOf(mapping.get("Type"));
         mDescription = mapping.get("Description");
     }
@@ -85,7 +88,7 @@ public class VCFInfoHeaderLine extends VCFHeaderLine {
         else if (mVersion == VCFHeaderVersion.VCF4_0) {
             Map<String,Object> map = new LinkedHashMap<String,Object>();
             map.put("ID",mName);
-            map.put("Number",mCount == UNBOUNDED ? UNBOUNDED_ENCODING : mCount);
+            map.put("Number",mCount == UNBOUNDED ? (mVersion == VCFHeaderVersion.VCF4_0 ? UNBOUNDED_ENCODING_VCF4 : UNBOUNDED_ENCODING_VCF3) : mCount);
             map.put("Type",mType);
             map.put("Description",mDescription);
             return "INFO=" + VCFHeaderLineTranslator.toValue(this.mVersion,map);
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
index e21697640..d4106b78e 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
@@ -34,6 +34,17 @@ public class VCFHeaderUnitTest extends BaseTest {
         checkMD5ofHeaderFile(codec, "5873e029bd50d6836b86438bccd15456");
     }
 
+    @Test
+    public void testVCF4ToVCF3Alternate() {
+        VCF4Codec codec = new VCF4Codec();
+        List<String> headerFields = new ArrayList<String>();
+        for (String str : VCF3_3headerStrings_with_negitiveOne)
+            headerFields.add(str);
+        Assert.assertEquals(17,codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
+        codec.getHeader(VCFHeader.class).setVersion(VCFHeaderVersion.VCF3_3);
+        checkMD5ofHeaderFile(codec, "e750fd0919704d10813dfe57ac1a0df3");
+    }
+
     @Test
     public void testVCF4ToVCF4() {
         VCF4Codec codec = new VCF4Codec();
@@ -44,6 +55,16 @@ public class VCFHeaderUnitTest extends BaseTest {
         checkMD5ofHeaderFile(codec, "4648aa1169257e0a8a9d30131adb5f35");
     }
 
+    @Test
+    public void testVCF4ToVCF4_alternate() {
+        VCF4Codec codec = new VCF4Codec();
+        List<String> headerFields = new ArrayList<String>();
+        for (String str : VCF3_3headerStrings_with_negitiveOne)
+            headerFields.add(str);
+        Assert.assertEquals(17, codec.createHeader(headerFields, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
+        checkMD5ofHeaderFile(codec, "ad8c4cf85e868b0261ab49ee2c613088");
+    }
+
     private void checkMD5ofHeaderFile(VCF4Codec codec, String md5sum) {
         File myTempFile = null;
         PrintWriter pw = null;
@@ -81,4 +102,23 @@ public class VCFHeaderUnitTest extends BaseTest {
                 "##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
                 "##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
                 };
+
+    public String[] VCF3_3headerStrings_with_negitiveOne = {
+                "##fileformat=VCFv4.0",
+                "##filedate=2010-06-21",
+                "##reference=NCBI36",
+                "##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
+                "##INFO=<ID=YY, Number=., Type=Integer, Description=\"Some weird value that has lots of parameters\">",
+                "##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
+                "##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">",
+                "##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">",
+                "##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">",
+                "##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">",
+                "##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">",
+                "##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">",
+                "##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
+                "##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
+                "##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
+                "##FORMAT=<ID=TT, Number=., Type=Integer, Description=\"Lots of TTs\">",
+                };
 }