diff --git a/SNPsplit b/SNPsplit
index 46b50e9..f7a41d4 100755
--- a/SNPsplit
+++ b/SNPsplit
@@ -22,10 +22,8 @@ use Cwd;
 ## You should have received a copy of the GNU General Public License
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-# June 16: making changes to skip tag2sort
-
 ## Reading in a BAM or SAM file
-my $pipeline_version = '0.3.4_dev';
+my $pipeline_version = '0.4.0';
 my $parent_dir = getcwd;
 my $full_commandline = join (" ","SNPsplit",@ARGV);
 # warn "Full commandline: $full_commandline\n"; sleep(5);
diff --git a/SNPsplit_genome_preparation b/SNPsplit_genome_preparation
index bf13bb1..cac09ed 100755
--- a/SNPsplit_genome_preparation
+++ b/SNPsplit_genome_preparation
@@ -29,7 +29,7 @@ use Cwd;
 # Modifying 30 June 2020
 
 ## Reading in a BAM or SAM file
-my $pipeline_version = '0.3.3dev';
+my $pipeline_version = '0.4.0';
 my $parent_dir = getcwd();
 my ($vcf_file,$strain,$strain2,$strain_index,$strain2_index,$genome_folder,$skip_filtering,$nmasking,$full_sequence,$dual_hybrid,$genome_build) = process_commandline ();