diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index 8c95091a6..69920ece4 100644
--- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Arrays;
 
@@ -198,7 +199,9 @@ public class BaseUtils {
      * @param base [AaCcGgTt]
      * @return 0, 1, 2, 3, or -1 if the base can't be understood
      */
-    static public int simpleBaseToBaseIndex(byte base) {
+    static public int simpleBaseToBaseIndex(final byte base) {
+        if ( base < 0 || base >= 256 )
+            throw new UserException.BadInput("Non-standard bases were encountered in either the input reference or BAM file(s)");
         return baseIndexMap[base];
     }