diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
index 811db71444c10ef17e0302c6ac9519f708ce98cd..e1a06ee2db93963eb57f54425ee63e05d4563912 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFFilter.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -550,7 +550,7 @@ public class VCFFilter extends JFrame
               
               if(sampleIndex > -1) // look at a specific sample
               {
-                if( !recFilter.pass(record, samples[sampleIndex].split(","), vcfReader))
+                if(samples[sampleIndex] == null || !recFilter.pass(record, samples[sampleIndex].split(","), vcfReader))
                   return false;
               }
               else                 // look at all samples