#!/usr/bin/env perl

use strict;
use warnings;

my %tmp;

while (<DATA>) {
    chomp;
    my ($k0, $k, $v) = (split /\t/)[0, 2, 5];
    $tmp{$k0}{k} = exists $tmp{$k0}{k} ? join ',' => $tmp{$k0}{k}, $k : $k;
    $tmp{$k0}{v} = exists $tmp{$k0}{v} ? join ',' => $tmp{$k0}{v}, $v : $v;
}

my %out = map { $_ => { $tmp{$_}{k} => $tmp{$_}{v} } } keys %tmp;

# For testing
use Data::Dumper;
print Dumper \%out;

__DATA__
p1  X   cis X   X   10
p1  X   plat    X   X   20
p1  X   gls X   X   NA
p2  X   cis X   X   0
p2  X   NA  X   X   9

##</code><code>##

$VAR1 = {
          'p1' => {
                    'cis,plat,gls' => '10,20,NA'
                  },
          'p2' => {
                    'cis,NA' => '0,9'
                  }
        };