diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 6bb894323..8ab36050b 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -275,6 +275,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         headerInfo.add(new VCFInfoHeaderLine("extType", 1, VCFHeaderLineType.String, "Extended type of event: SNP, MNP, INDEL, or COMPLEX"));
         headerInfo.add(new VCFInfoHeaderLine("QDE", 1, VCFHeaderLineType.Float, "QD value divided by the number of variants found on the haplotype that contained this variant"));
 
+        // FILTER fields are added unconditionally as it's not always 100% certain the circumstances
+        // where the filters are used.  For example, in emitting all sites the lowQual field is used
+        headerInfo.add(new VCFFilterHeaderLine(UnifiedGenotyperEngine.LOW_QUAL_FILTER_NAME, "Low quality"));
+
         vcfWriter.writeHeader(new VCFHeader(headerInfo, samples));
 
         try {
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index a87703423..6fdfb83e4 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -20,17 +20,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "7b4e76934e0c911220b4e7da8776ab2b");
+        HCTest(CEUTRIO_BAM, "", "882ece8391cfec30ab658970a487d078");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() {
-        HCTest(NA12878_BAM, "", "fcf0cea98a571d5e2d1dfa8b5edc599d");
+        HCTest(NA12878_BAM, "", "6f458e04251bc4c09b5b544d46f19d68");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
-        HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "ff370c42c8b09a29f1aeff5ac57c7ea6");
+        HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "c172791007f867bf3b975d4194564d9e");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -41,7 +41,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex() {
-        HCTestComplexVariants(CEUTRIO_BAM, "", "6f9fda3ea82c5696bed1d48ee90cd76b");
+        HCTestComplexVariants(CEUTRIO_BAM, "", "94186811016b332a58c150df556278f8");
     }
 
 }