diff --git a/CHANGES.md b/CHANGES.md
index e07be09..308c594 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.9.0
+- Masking of pindel calls where ref == alt implemented to remove invalid calls from pindel output
+  - Core pindel fix required to resolve the underlying problem
+
 ## 3.8.0
 
 - Adds `-noflag` option to `pindel.pl` for use cases where flagging needs to be executed separately or not at all.
diff --git a/perl/lib/Sanger/CGP/Pindel.pm b/perl/lib/Sanger/CGP/Pindel.pm
index 74c5c5b..512a6e1 100644
--- a/perl/lib/Sanger/CGP/Pindel.pm
+++ b/perl/lib/Sanger/CGP/Pindel.pm
@@ -33,7 +33,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.8.0';
+our $VERSION = '3.9.0';
 our @EXPORT = qw($VERSION);
 
 1;