Just noticed that the efficient conversion to uppercase method is redundant since it's already implemented efficiently in Picard; let's just have a single implementation.

public/java/src/org/broadinstitute/sting/utils/BaseUtils.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.utils;
 
+import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.util.Arrays;
@@ -444,29 +445,8 @@ public class BaseUtils {
      * @param bases   the bases
      * @return the upper cased version
      */
-    static public byte[] convertToUpperCase(final byte[] bases) {
+    static public void convertToUpperCase(final byte[] bases) {
-        for ( int i = 0; i < bases.length; i++ ) {
+        StringUtil.toUpperCase(bases);
-            if ( (char)bases[i] >= 'a' )
-                bases[i] = toUpperCaseBase(bases[i]);
-        }
-        return bases;
-    }
-
-    static public byte toUpperCaseBase(final byte base) {
-        switch (base) {
-            case 'a':
-                return 'A';
-            case 'c':
-                return 'C';
-            case 'g':
-                return 'G';
-            case 't':
-                return 'T';
-            case 'n':
-                return 'N';
-            default:
-                return base;
-        }
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java

@@ -105,7 +105,7 @@ public class Allele implements Comparable<Allele> {
             if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele");
         }
         else {
-            bases = BaseUtils.convertToUpperCase(bases);
+            BaseUtils.convertToUpperCase(bases);
         }
 
         this.isRef = isRef;