So, if I understand correctly, you want your results to look something like:

$data{"HG00553"}[162][16287215] = "0 0"
$data{"HG00553"}[162][16287226] = "0 0"
...
$data{"HG00638"}[162][16287851] = "1 1"
...
[download]

First, I'd suggest you do a little debug work to understand what your code is doing. Specifically:

while (<$in_file>) {
    print "$_";
    chomp;
    my @snp_bins;
    if (/^SAMPLE/) {
        my ( $placeholder, @coords ) = split /,/;
        foreach my $coord (@coords) {
            push @snp_bins, int( $coord / 100_000 );
        }
    }
    else {
        my ( $id, @snps ) = split /,/;
        push @individuals, $id;
        foreach my $individual (@individuals) {
            print "working on $individual\n";
            foreach my $snp (@snps) {
                my $snp_bin = shift @snp_bins;
                print "snp_bin $snp_bin\n";
                $data{$individual}[ [ $snp_bin ] ] = $snp;
            }

        }
        print "snp_bins: @snp_bins\n";
    }
}
[download]

I think that you'll find some things which you didn't expect. Also, I think that you might be better off using HoHoH instead. I believe that doing:

$data{$individual}[162] = "something"
[download]

will result in:

$data{$individual}[0..162]
[download]

even though you are only concerned with the former. So it would probably be better to:

$data{$individual}{162}{16287215} = "0 0"
[download]

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