diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 4e5ad47cb96e439ba60e9846392646554a1fb0b4..a5565df5b7423c451286c035ee52f7f7871058e0 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -91,6 +91,8 @@ class IOUtils
     try
     {
       File filterFile = getFile(vcfFileName, nfiles, ".filter", null);
+      if(filterFile == null)
+        return null;
       FileWriter writer = new FileWriter(filterFile);
       AbstractVCFReader.write(vcfFileName, writer, vcfView, features);
 
@@ -150,6 +152,8 @@ class IOUtils
     for(int i=0; i<vcfFiles.size(); i++)
     {
       File filterFile = IOUtils.writeVCF(vcfFiles.get(i), vcfView, features, vcfFiles.size());
+      if(filterFile == null)
+        return;
       filterFiles += filterFile.getAbsolutePath()+"\n";
     }