ALTERNATE INTERPRETATION OF OP's DESIRES; namely, that cristianro87 wants to summarize ALL the data elements:

#!/usr/bin/perl
use warnings;
use strict;
use 5.016;

# 1087978

while (<DATA>) {
    my ($chrom, $pos, $id, $ref, $alt, $qual);
    if ($_ =~ /#CHROM.+/ ) {           # title "Load table with row/co
+lumn names" 
        next;                          # does NOT match "access the el
+ements" example
    } elsif ( $_ eq '' ) {
        last;
    } else {
        ($chrom, $pos, $id, $ref, $alt, $qual) = split;
        # desired out: [chr1][1092482][REF] = T
        say "[$chrom] [$pos] [REF] = " . $alt; 
    }
}

=head  execution

C:\>1087978.pl
[chr1] [1092344] [REF] = T
[chr1] [1092367] [REF] = T
[chr1] [1092400] [REF] = C
[chr1] [1092424] [REF] = G
[chr1] [1092461] [REF] = A
[chr1] [1092470] [REF] = G
[chr1] [1092482] [REF] = C
[chr1] [1093235] [REF] = A
[chr1] [1093245] [REF] = T

=cut

__DATA__
#CHROM    POS    ID    REF    ALT    QUAL
chr1    1092344    .    G    T    79.54
chr1    1092367    .    C    T    148.50
chr1    1092400    .    G    C    90.54
chr1    1092424    .    A    G    93.14
chr1    1092461    .    G    A    105.30
chr1    1092470    .    T    G    103.06
chr1    1092482    .    T    C    104.33
chr1    1093235    .    G    A    16.08
chr1    1093245    .    C    T    244.75
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Far simpler: no hashes but possibly (caveat here ->) a simple-minded interp of an unclear SOPW.