Try this to see if it's what you need:

use strict;
use warnings;
use Data::Dumper;

my @array = ();
while (my $line = <$ifh>) {
  push(@array, [ (split(/\t/, $line))[0,3,7] ]);
}

print Dumper(\@array);
[download]

Update: BTW, in your spec, you say the 1st, 4th, and 8th column, but in your output data you show the 1st, 3rd and 8th columns. Which is it?

Update: I see that you have updated your root node to reflect the corrected indices. Generally, it is considered to be polite to indicate (via an Update: such as this) that you have changed the wording/context of your node. Otherwise, it makes the respondents look like *they* made the mistake.