diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 53e6152e69b1d59ae79a6bba7afa557b873595ab..1378391cae4bc695b3420ba176848a0cd04a85bf 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -430,7 +430,11 @@ public class BamView extends JPanel
    * @throws IOException
    */
   private SAMFileReader getSAMFileReader(final String bam) throws IOException
-  {  
+  {
+    // parsing of the header happens during SAMFileReader construction, 
+    // so need to set the default stringency
+    SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
+    
     if(samFileReaderHash.containsKey(bam))
       return samFileReaderHash.get(bam);