diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index c47c2504c62b1763e292d64c82593ad66bf15123..c892521651072d4d39690ff4f255b81d678b4ede 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -420,7 +420,7 @@ public class BamView extends JPanel
         // Use Picard to index the file
         // requires reads to be sorted by coordinate
         new BuildBamIndex().instanceMain(
-          new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000" });
+          new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000", "VALIDATION_STRINGENCY=LENIENT" });
       }
       catch(SAMException e)
       {