diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index 75bbff21d..7f6b5d4d4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -63,7 +63,7 @@ public class AlleleBalance implements InfoFieldAnnotation, StandardAnnotation {
                 continue;
 
             if ( vc.isSNP() ) {
-                final String bases = new String(context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases()).toUpperCase();
+                final String bases = new String(context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases());
                 if ( bases.length() == 0 )
                     return null;
                 char refChr = vc.getReference().toString().charAt(0);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 70f674657..2dbe70c09 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -55,14 +55,14 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
 
         int leftRun = 0;
         for ( int i = refBasePos - 1; i >= 0; i--) {
-            if ( Character.toUpperCase(bases[i]) != altAllele )
+            if ( bases[i] != altAllele )
                 break;
             leftRun++;
         }
 
         int rightRun = 0;
         for ( int i = refBasePos + 1; i < bases.length; i++) {
-            if ( Character.toUpperCase(bases[i]) != altAllele )
+            if ( bases[i] != altAllele )
                 break;
             rightRun++;
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 4faa513be..76813661c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -115,7 +115,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         if ( verboseWriter != null ) {
             StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t");
             for ( byte altAllele : BaseUtils.BASES ) {
-                //char base = Character.toUpperCase(altAllele);
                 header.append("POfDGivenAFFor" + (char)altAllele + "\t");
                 header.append("PosteriorAFFor" + (char)altAllele + "\t");
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 1983b3cc9..fedc39efc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -123,7 +123,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
         if ( pileup != null ) {
 
             int mismatchQualities = 0, totalQualities = 0;
-            char refBase = (char)ref.getBase();
+            byte refBase = ref.getBase();
             for (PileupElement p : pileup ) {
                 // check the ends of the reads to see how far they extend
                 SAMRecord read = p.getRead();
@@ -136,7 +136,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
 
                 // look for mismatches
                 else {
-                    if ( Character.toUpperCase(p.getBase()) != refBase )
+                    if ( p.getBase() != refBase )
                         mismatchQualities += p.getQual();
                     totalQualities += p.getQual();
                 }
diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 3b4154549..121a334a3 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -195,9 +195,6 @@ public class AlignmentUtils {
                         byte readChr = readBases[readIndex];
                         if ( readChr != refChr )
                             sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
-//                        char readChr = (char)readBases[readIndex];
-//                        if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
-//                            sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
                     }
                     break;
                 case I: