diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index 941b11b36..93df9f091 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -427,7 +427,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
         if ( qual > SAMUtils.MAX_PHRED_SCORE )
             throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")");
         if ( capBaseQualsAtMappingQual )
-            qual = (byte)Math.min((int)qual, p.getMappingQual());
+            qual = (byte) Math.min( 0xff & qual, p.getMappingQual());
         if ( (int)qual < minBaseQual )
             qual = (byte)0;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 76ad61b77..c3e7276a6 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -137,7 +137,7 @@ public class LikelihoodCalculationEngine {
             final byte[] readInsQuals = read.getBaseInsertionQualities();
             final byte[] readDelQuals = read.getBaseDeletionQualities();
             for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
-                readQuals[kkk] = ( readQuals[kkk] > (byte) read.getMappingQuality() ? (byte) read.getMappingQuality() : readQuals[kkk] ); // cap base quality by mapping quality
+                readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
                 //readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated
                 //readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated
                 // TODO -- why is Q18 hard-coded here???