diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 3cc058e92..a417a6b62 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -193,11 +193,12 @@ public class VariantContextAdaptors {
                 if ( vcfG.isFiltered() ) // setup the FL genotype filter fields
                     genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFGenotypeRecord.GENOTYPE_FILTER_KEY).split(";")));
 
-                Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, vcfG.getNegLog10PError(), genotypeFilters, fields, vcfG.getPhaseType() == VCFGenotypeRecord.PHASE.PHASED);
+                double qual = vcfG.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();
+                Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, qual, genotypeFilters, fields, vcfG.getPhaseType() == VCFGenotypeRecord.PHASE.PHASED);
                 genotypes.put(g.getSampleName(), g);
             }
 
-            double qual = vcf.getQual() == -1 ? VariantContext.NO_NEG_LOG_10PERROR : vcf.getNegLog10PError();
+            double qual = vcf.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcf.getNegLog10PError();
             VariantContext vc = new VariantContext(name, vcf.getLocation(), alleles, genotypes, qual, filters, attributes);
             vc.validate();
             return vc;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
index 2a9050f4d..d9ad01a0f 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
@@ -127,8 +127,20 @@ public class VCFGenotypeRecord {
         return mFields;
     }
 
+    /**
+     * @return the phred-scaled quality score
+     */
+    public double getQual() {
+        return ( mFields.containsKey(GENOTYPE_QUALITY_KEY) ? Double.valueOf(mFields.get(GENOTYPE_QUALITY_KEY)) : MISSING_GENOTYPE_QUALITY);
+    }
+
+    public boolean isMissingQual() {
+        return (int)getQual() == MISSING_GENOTYPE_QUALITY;
+    }
+
     public double getNegLog10PError() {
-        return ( mFields.containsKey(GENOTYPE_QUALITY_KEY) ? Double.valueOf(mFields.get(GENOTYPE_QUALITY_KEY)) / 10.0 : MISSING_GENOTYPE_QUALITY);
+        double qual = getQual();
+        return (qual == MISSING_GENOTYPE_QUALITY ? MISSING_GENOTYPE_QUALITY : qual / 10.0);
     }
 
     public int getReadCount() {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index e71202cd3..11c24847e 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -39,6 +39,7 @@ public class VCFRecord {
     public static final String EMPTY_ID_FIELD = ".";
     public static final String EMPTY_ALLELE_FIELD = ".";
     public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
+    public static final int MISSING_GENOTYPE_QUALITY = -1;
 
     // the reference base
     private String mReferenceBases;
@@ -350,6 +351,10 @@ public class VCFRecord {
         return mQual;
     }
 
+    public boolean isMissingQual() {
+        return (int)mQual == MISSING_GENOTYPE_QUALITY;
+    }
+
     /**
      * @return the -log10PError
      */
@@ -448,8 +453,8 @@ public class VCFRecord {
     }
 
     public void setQual(double qual) {
-        if ( qual < 0 && MathUtils.compareDoubles(qual, -1.0) != 0 )
-            throw new IllegalArgumentException("Qual values cannot be negative unless they are -1 ('unknown')");
+        if ( qual < 0 && (int)qual != MISSING_GENOTYPE_QUALITY )
+            throw new IllegalArgumentException("Qual values cannot be negative unless they are " + MISSING_GENOTYPE_QUALITY + " ('unknown')");
         mQual = qual;
     }
 
@@ -555,8 +560,8 @@ public class VCFRecord {
             builder.append(EMPTY_ALLELE_FIELD);
         }
         builder.append(FIELD_SEPERATOR);
-        if ( MathUtils.compareDoubles(mQual, -1.0) == 0 )
-            builder.append("-1");
+        if ( (int)mQual == MISSING_GENOTYPE_QUALITY )
+            builder.append(MISSING_GENOTYPE_QUALITY);
         else
             builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, mQual));
         builder.append(FIELD_SEPERATOR);