If your program output a file, why use a backtick? simply use a open function in Perl, like this:

use warnings;
use strict;

my $output_file="output.bam";
open my $fh,'>',$output_file or die "can't open $output_file:$!";
   print $fh " ... hello world into my file...";
close $fh or die "can close file: $!";
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Please, check perldoc perlopentut
or perldoc -f open for more ...
Hope this helps