Code

#!/usr/bin/env perl

use strict;
use warnings;

#Variable
my $file1 = '/home//Desktop/file1.txt';
my $file2 = '/home/Desktop/file2.txt';

#Filehandle
open( my $FH , '<', $file1 ) or die "Couldn't open file \"$file1\": $!\n";
open( my $FH , '<', $file2 ) or die "Couldn't open file \"$file2\": $!\n";

#Program for reading dbsnp
my @file1_rows = split ("\t", $file1);

...