diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java
index fc0c4c69b..b9da136dc 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java
@@ -73,7 +73,7 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
     }
 
     public boolean isMismatch( SAMRecord read, int offset, ReferenceContext ref ) {
-        return ((char) read.getReadBases()[offset]) == ref.getBase();
+        return (Character.toUpperCase((char) read.getReadBases()[offset]) != ref.getBase());
     }
 
     public int getQScoreAsInt( SAMRecord read, int offset ) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSCovariantByCountsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSCovariantByCountsWalker.java
index 4ba0e279c..664b10789 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSCovariantByCountsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSCovariantByCountsWalker.java
@@ -111,7 +111,7 @@ public class NQSCovariantByCountsWalker extends LocusWalker< LocalMapType, int[]
     }
 
     public boolean isMismatch( SAMRecord read, int offset, ReferenceContext ref ) {
-        return ( ((char)read.getReadBases()[offset]) == ref.getBase() );
+        return ( Character.toUpperCase((char)read.getReadBases()[offset]) != ref.getBase() );
     }
 
     public String header() {