diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index 627bee3ea..dee282056 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -1000,7 +1000,7 @@ public class GATKVariantContextUtils {
     public static VariantContext trimAlleles(final VariantContext inputVC, final boolean trimForward, final boolean trimReverse) {
         if ( inputVC == null ) throw new IllegalArgumentException("inputVC cannot be null");
 
-        if ( inputVC.getNAlleles() <= 1 )
+        if ( inputVC.getNAlleles() <= 1 || inputVC.isSNP() )
             return inputVC;
 
         // see whether we need to trim common reference base from all alleles
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
index ff42abb23..fcc7c7998 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -694,6 +694,15 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
                         root.alleles(Arrays.asList(CAref, C)).stop(11).make(),
                         root.alleles(Arrays.asList(CAAAref, C)).stop(13).make())});
 
+        final Allele threeCopies = Allele.create("GTTTTATTTTATTTTA", true);
+        final Allele twoCopies = Allele.create("GTTTTATTTTA", true);
+        final Allele zeroCopies = Allele.create("G", false);
+        final Allele oneCopies = Allele.create("GTTTTA", false);
+        tests.add(new Object[]{root.alleles(Arrays.asList(threeCopies, zeroCopies, oneCopies)).stop(25).make(),
+                Arrays.asList(
+                        root.alleles(Arrays.asList(threeCopies, zeroCopies)).stop(25).make(),
+                        root.alleles(Arrays.asList(twoCopies, zeroCopies)).stop(20).make())});
+
         return tests.toArray(new Object[][]{});
     }