diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 23a296b77ef74bf130fa8fa946463133d3f04321..241f1184611cf2462fe1982d696b6a4b9957be8c 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -508,7 +508,11 @@ class VCFRecord
     {
       String alt = getAlt().toString();
       if(vcf_v4)
+      {
+        if(alt.equals("."))
+          return getRef().length();
         return getRef().length()-alt.length();
+      }
       
       int index = alt.indexOf("D");
       int ndel = 0;