GetOptions(
    'u|unique' => \my $unique,
);
open F,'/Users/gupta567varun/Desktop/AAC_SJ.out.tab',or die $!;
while(<F>){
    chomp;
    my @s = split /\t/,$_;
    my $count = $s[6];
    if($count > $unique){
        print $_,"\n";
    }
}
close F;
[download]

Thanks for pointing me out the documentation. What is wrong here in the code. I ran it like this perl script.pl -u 4 , but it still prints lines less than 4?? EDIT:

#!/usr/bin/perl-w
use strict;
use warnings;
use Getopt::Long;

GetOptions(
    'uniq=i' => \my $unique,
);
while(<>){
    chomp;
    my @s = split /\t/,$_;
    my $count = $s[6];
    if($count > $unique){
        print $_,"\n";
    }
}
[download]

Running the script as

perl script.pl --uniq 4 file.txt

Works now!! Thanks