diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
index e87986a2e..903133ffa 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
@@ -92,10 +92,13 @@ public class AnnotatorInputTableCodec implements ReferenceDependentFeatureCodec<
 
         GenomeLoc loc;
         String chr = st.nextToken();
-        if ( chr.indexOf(":") != -1 )
+        if ( chr.indexOf(":") != -1 ) {
             loc = genomeLocParser.parseGenomeInterval(chr);
-        else
+        } else {
+            if ( st.countTokens() < 3 )
+                throw new CodecLineParsingException("Couldn't parse GenomeLoc out of the following line because there aren't enough tokens.\nLine: " + line);
             loc = genomeLocParser.createGenomeLoc(chr, Integer.valueOf(st.nextToken()), Integer.valueOf(st.nextToken()));
+        }
         return new AnnotatorInputTableFeature(loc.getContig(), (int)loc.getStart(), (int)loc.getStop());
     }