diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index f513b3345..fd0cf7869 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -203,7 +203,11 @@ public class UserException extends ReviewedStingException {
 
     public static class MalformedVCF extends UserException {
         public MalformedVCF(String message, String line) {
-            super(String.format("The provided VCF file is malformed at approximately line %s: %s", line, message));
+            super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
+        }
+
+        public MalformedVCF(String message) {
+            super(String.format("The provided VCF file is malformed: %s", message));
         }
 
         public MalformedVCF(String message, int lineNo) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index d950a4541..8494b9570 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -28,6 +28,7 @@ import org.broad.tribble.TribbleException;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.EnumMap;
 
@@ -149,8 +150,12 @@ public class GenotypeLikelihoods {
         if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
             String[] strings = likelihoodsAsString_PLs.split(",");
             double[] likelihoodsAsVector = new double[strings.length];
-            for ( int i = 0; i < strings.length; i++ ) {
-                likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0;
+            try {
+                for ( int i = 0; i < strings.length; i++ ) {
+                    likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0;
+                }
+            } catch (NumberFormatException e) {
+                throw new UserException.MalformedVCF("The GL/PL tag contains non-integer values");
             }
             return likelihoodsAsVector;
         } else