diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index c2c08fe9799a71302af140987abaa88f59c66ec0..b5be95af4d02c58236e48f714cf06cff8c42050c 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -402,7 +402,11 @@ public class BamView extends JPanel
     {
       bamIndexFile = new File(bam + ".bai");
       if(!bamIndexFile.exists())
-        bamIndexFile = new File(bam + ".crai");
+      {
+        final File cramIndexFile = new File(bam + ".crai");
+        if(cramIndexFile.exists())
+          return cramIndexFile;
+      }
     }
 
     return bamIndexFile;