$ perl -Mstrict -Mwarnings -MData::Dumper -E '
> open my $tableFH, q{<}, \ <<EOD or die $!;
> #CHROM    POS    ID    REF    ALT    QUAL
> chr1    1092344    .    G    T    79.54
> chr1    1092367    .    C    T    148.50
> chr1    1092400    .    G    C    90.54
> chr1    1092424    .    A    G    93.14
> chr1    1092461    .    G    A    105.30
> chr1    1092470    .    T    G    103.06
> chr1    1092482    .    T    C    104.33
> chr1    1093235    .    G    A    16.08
> chr1    1093245    .    C    T    244.75
> chr2    1347864    .    T    C    107.34
> chr2    1456284    .    A    C    86.32
> chr3    2031473    .    G    T    25.34
> chr3    2256801    .    C    T    154.65
> EOD
> 
> my( undef, undef, @cols ) = map { split } scalar <$tableFH>;
> my %chroms;
> 
> while ( <$tableFH> )
> {
>     my( $chr, $pos, @vals ) = split;
>     @{ $chroms{ $chr }->{ $pos } }{ @cols } = @vals;
> }
> 
> print Data::Dumper->Dumpxs( [ \ %chroms ], [ qw{ *chroms } ] );'

##</code><code>##

%chroms = (
            'chr3' => {
                        '2031473' => {
                                       'QUAL' => '25.34',
                                       'ID' => '.',
                                       'ALT' => 'T',
                                       'REF' => 'G'
                                     },
                        '2256801' => {
                                       'QUAL' => '154.65',
                                       'ID' => '.',
                                       'ALT' => 'T',
                                       'REF' => 'C'
                                     }
                      },
            'chr1' => {
                        '1093245' => {
                                       'QUAL' => '244.75',
                                       'ID' => '.',
                                       'ALT' => 'T',
                                       'REF' => 'C'
                                     },
                        '1092344' => {
                                       'QUAL' => '79.54',
                                       'ID' => '.',
                                       'ALT' => 'T',
                                       'REF' => 'G'
                                     },
                        '1092461' => {
                                       'QUAL' => '105.30',
                                       'ID' => '.',
                                       'ALT' => 'A',
                                       'REF' => 'G'
                                     },
                        '1093235' => {
                                       'QUAL' => '16.08',
                                       'ID' => '.',
                                       'ALT' => 'A',
                                       'REF' => 'G'
                                     },
                        '1092367' => {
                                       'QUAL' => '148.50',
                                       'ID' => '.',
                                       'ALT' => 'T',
                                       'REF' => 'C'
                                     },
                        '1092424' => {
                                       'QUAL' => '93.14',
                                       'ID' => '.',
                                       'ALT' => 'G',
                                       'REF' => 'A'
                                     },
                        '1092470' => {
                                       'QUAL' => '103.06',
                                       'ID' => '.',
                                       'ALT' => 'G',
                                       'REF' => 'T'
                                     },
                        '1092400' => {
                                       'QUAL' => '90.54',
                                       'ID' => '.',
                                       'ALT' => 'C',
                                       'REF' => 'G'
                                     },
                        '1092482' => {
                                       'QUAL' => '104.33',
                                       'ID' => '.',
                                       'ALT' => 'C',
                                       'REF' => 'T'
                                     }
                      },
            'chr2' => {
                        '1456284' => {
                                       'QUAL' => '86.32',
                                       'ID' => '.',
                                       'ALT' => 'C',
                                       'REF' => 'A'
                                     },
                        '1347864' => {
                                       'QUAL' => '107.34',
                                       'ID' => '.',
                                       'ALT' => 'C',
                                       'REF' => 'T'
                                     }
                      }
          );