Nothing wrong with cut or calling unix commands in general but may as well use the normal Perl commands once you've started. In particular, look into split so for each file you could do something like:

@a = split(/\t/);
print "$a[0]\t$a[1]\t$a[12]\t$a[11]\n";
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There are fancier ways to do this but seems like it'd be best to keep it simple to begin with. The other parts depend on whether you are writing all results to a single file or operating on each file individually, etc.