diff --git a/perl/sortByRef.pl b/perl/sortByRef.pl
new file mode 100755
index 000000000..7696be3ba
--- /dev/null
+++ b/perl/sortByRef.pl
@@ -0,0 +1,109 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+sub usage {
+
+    print "\nUsage:\n";
+    print "sortByRef.pl [--k POS] INPUT REF_DICT\n\n";
+
+    print " Sorts lines of the input file INFILE according\n";
+    print " to the reference contig order specified by the\n";
+    print " reference dictionary REF_DICT (.fai file).\n";
+    print " The sort is stable. If -k option is not specified,\n";
+    print " it is assumed that the contig name is the first\n";
+    print " field in each line.\n\n";
+    print "  --k POS :  contig name is in the field POS (1-based)\n";
+    print "             of input lines.\n\n";
+
+    exit(1);
+}
+
+my $pos = 1;
+GetOptions( "k:i" => \$pos );
+
+$pos--;
+
+usage() if ( scalar(@ARGV) == 0 );
+
+if ( scalar(@ARGV) != 2 ) {
+    print "Wrong number of arguments\n";
+    usage();
+}
+
+my $input_file = $ARGV[0];
+my $dict_file = $ARGV[1];
+
+open(DICT, "< $dict_file") or die("Can not open $dict_file: $!");
+
+my %ref_order;
+
+my $n = 0;
+while ( <DICT> ) {
+    chomp;
+    my ($contig, $rest) = split "\t";
+    die("Dictionary file is probably corrupt: multiple instances of contig $contig") if ( defined $ref_order{$contig} );
+
+    $ref_order{$contig} = $n;
+    $n++;
+}
+
+close DICT;
+#we have loaded contig ordering now
+
+open(INPUT, "< $input_file") or die("Can not open $input_file: $!");
+
+my %temp_outputs;
+
+while ( <INPUT> ) {
+    
+    my @fields = split '\s';
+    die("Specified field position exceeds the number of fields:\n$_") 
+        if ( $pos >= scalar(@fields) );
+
+    my $contig = $fields[$pos];
+    chomp $contig if ( $pos == scalar(@fields) - 1 ); # if last field in line
+
+    my $order;
+    if ( defined $ref_order{$contig} ) { $order = $ref_order{$contig}; }
+    else {
+        $order = $n; # input line has contig that was not in the dict; 
+        $n++; # this contig will go at the end of the output, 
+              # after all known contigs
+    }
+
+    my $fhandle;
+    if ( defined $temp_outputs{$order} ) { $fhandle = $temp_outputs{$order} }
+    else {
+        open( $fhandle, " > /tmp/sortByRef.$$.$order.tmp" ) or
+            die ( "Can not open temporary file $order: $!");
+        $temp_outputs{$order} = $fhandle;
+    }
+
+    # we got the handle to the temp file that keeps all 
+    # lines with contig $contig
+
+    print $fhandle $_; # send current line to its corresponding temp file
+}
+
+close INPUT;
+
+foreach my $f ( values %temp_outputs ) { close $f; }
+
+# now collect back into single output stream:
+
+for ( my $i = 0 ; $i < $n ; $i++ ) {
+    # if we did not have any lines on contig $i, then there's 
+    # no temp file and nothing to do
+    next if ( ! defined $temp_outputs{$i} ) ; 
+
+    my $f; 
+    open ( $f, "< /tmp/sortByRef.$$.$i.tmp" );
+    while ( <$f> ) { print ; }
+    close $f;
+
+    unlink "/tmp/sortByRef.$$.$i.tmp";
+
+    
+}