my $index = 'path/to/file/file.name';
tie (@master, 'Tie::File', $masterList) or die "Can't tie $masterList";

foreach my $pos(@master){
        chomp $pos;
        my $quickLook = qx(grep '^$pos' $index);
        my @split = split(/\t/,$quickLook);
        print $tFile $split[1];
         push (@idxArray, $split[1]);
 }

##</code><code>##

1
2
3
4
6
8
10
12
15
17
etc...
3000000

##</code><code>##

1  atc
2 gca
3 att
4 ggc
5 aaa
etc...
29000000 ttg