while(){ chomp; my @current_line = split /\t/; push (@{$file2{$current_line[1]}}, $current_line[2]); if (exists $file1{$current_line[1]} ) { my $key = $current_line[1]; foreach my $position1 (@{$file1{$key}}){ if ($current_line[1] eq $key) { if ($current_line[2] == $position1) { if ($current_line[5] ==1) { if ($current_line[14] >= 3){ print RESULTS join ("\t", $current_line[1],$current_line[2],$current_line[5],$current_line[14], "***",$key, $position1), "\n"; push (@true_positives, $current_line[1]); } } } } } } }