diff --git a/perl/lib/PeakRescue.pm b/perl/lib/PeakRescue.pm
index 0d6a844..8da015f 100644
--- a/perl/lib/PeakRescue.pm
+++ b/perl/lib/PeakRescue.pm
@@ -3,7 +3,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '5.0.0';
+our $VERSION = '5.0.1';
 our @EXPORT = qw($VERSION);
 const my $LICENSE =>
 "#################
diff --git a/perl/lib/PeakRescue/RunPeakRescue.pm b/perl/lib/PeakRescue/RunPeakRescue.pm
index 6ba0c45..d20a5f1 100644
--- a/perl/lib/PeakRescue/RunPeakRescue.pm
+++ b/perl/lib/PeakRescue/RunPeakRescue.pm
@@ -191,7 +191,8 @@ sub _process_sam {
 		$cmd = "java -Xmx2G -jar $PICARD_PATH/ReorderSam.jar ".
 						"I= $tmp_combined_bam ".
 						"O= ".$self->options->{'kayrotypic'}.
-						" REFERENCE= ".$self->options->{'g'};
+						" REFERENCE= ".$self->options->{'g'}.
+						" ALLOW_CONTIG_LENGTH_DISCORDANCE= 1";
 										
 		PeakRescue::Base->_run_cmd($cmd);
 		Bio::DB::Bam->index_build($self->options->{'kayrotypic'});