diff --git a/pileup2baseindel.pl b/pileup2baseindel.pl
index 7dadecb..b2d07c0 100644
--- a/pileup2baseindel.pl
+++ b/pileup2baseindel.pl
@@ -72,7 +72,7 @@
 	
 	my @region=(3*($i-1),3*($i-1)+1,3*($i-1)+2);
 	my ($dp,$bases,$bq) = @dp_bases_bq[@region];
-	my $str = parsePileup($bases,$bq,$BQcut,$offset);
+	my $str = parsePileup($ref,$bases,$bq,$BQcut,$offset);
 	
 	if($str ne "*"){
 		print $fh join "\t",($chr,$loc,$ref,$str);
@@ -88,7 +88,7 @@
 		my $fh = $files{$i};
 		my @region=(3*($i-1),3*($i-1)+1,3*($i-1)+2);
 		my ($dp,$bases,$bq) = @dp_bases_bq[@region];
-		my $str = parsePileup($bases,$bq,$BQcut,$offset);
+		my $str = parsePileup($ref, $bases,$bq,$BQcut,$offset);
 		if($str ne "*"){
 			print $fh join "\t",($chr,$loc,$ref,$str);
 		}
@@ -103,7 +103,7 @@
 
 
 sub parsePileup{
-	my ($bases,$bq,$BQcut,$offset) = @_;
+	my ($ref,$bases,$bq,$BQcut,$offset) = @_;
 	
 	if($bases eq "*"){
 		return "*";