$ 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 } ] );'