diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
index 8c7bce6ac..73e129105 100644
--- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
+++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
@@ -673,7 +673,9 @@ public class BAQ {
         } else if ( excludeReadFromBAQ(read) ) {
             ; // just fall through
         } else {
-            if ( calculationType == CalculationMode.RECALCULATE || ! hasBAQTag(read) ) {
+            final boolean readHasBAQTag = hasBAQTag(read);
+
+            if ( calculationType == CalculationMode.RECALCULATE || ! readHasBAQTag ) {
                 if ( DEBUG ) System.out.printf("  Calculating BAQ on the fly%n");
                 BAQCalculationResult hmmResult = calcBAQFromHMM(read, refReader);
                 if ( hmmResult != null ) {
@@ -683,6 +685,9 @@ public class BAQ {
                         case DONT_MODIFY:     BAQQuals = hmmResult.bq; break;
                         default:              throw new ReviewedStingException("BUG: unexpected qmode " + qmode);
                     }
+                } else if ( readHasBAQTag ) {
+                    // remove the BAQ tag if it's there because we cannot trust it
+                    read.setAttribute(BAQ_TAG, null);
                 }
             } else if ( qmode == QualityMode.OVERWRITE_QUALS ) { // only makes sense if we are overwriting quals
                 if ( DEBUG ) System.out.printf("  Taking BAQ from tag%n");
diff --git a/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java
index 1e3386426..da82e9de5 100644
--- a/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java
@@ -203,6 +203,23 @@ public class BAQUnitTest extends BaseTest {
             Assert.assertTrue(baq.calcEpsilon( ref, alt, (byte)i) >= 0.0, "Failed to get baq epsilon range");
     }
 
+    @Test(enabled = true)
+    public void testBAQOverwritesExistingTagWithNull() {
+
+        // create a read with a single base off the end of the contig, which cannot be BAQed
+        final SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, fasta.getSequenceDictionary().getSequence("chr1").getSequenceLength() + 1, 1);
+        read.setReadBases(new byte[] {(byte) 'A'});
+        read.setBaseQualities(new byte[] {(byte) 20});
+        read.setCigarString("1M");
+        read.setAttribute("BQ", "A");
+
+        // try to BAQ and tell it to RECALCULATE AND ADD_TAG
+        BAQ baq = new BAQ(1e-3, 0.1, 7, (byte)4, false);
+        baq.baqRead(read, fasta, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.ADD_TAG);
+
+        // did we remove the existing tag?
+        Assert.assertTrue(read.getAttribute("BQ") == null);
+    }
 
     public void testBAQ(BAQTest test, boolean lookupWithFasta) {
         BAQ baqHMM = new BAQ(1e-3, 0.1, 7, (byte)4, false);         // matches current samtools parameters