Another possible solution... In this case, I just combined all your data into a single input for easier manipulation.

#!/usr/bin/perl

use strict;
use Data::Dumper;

my %chromosome;

while( <DATA> ) {
    my ($name, $pos, $val1, $val2) = split;
    if ( defined( $chromosome{$name}{$pos} )) {
        $chromosome{$name}{$pos}[0] = $chromosome{$name}{$pos}[0] + $v
+al1;
        $chromosome{$name}{$pos}[1] = $chromosome{$name}{$pos}[1] + $v
+al2;
    }
    else {
        $chromosome{$name}{$pos} = [$val1, $val2];
    }
}

print Dumper(\%chromosome);

__DATA__
chromosome1 50000 12 20
chromosome2 20000 0 21
chromosome3 41444 9 2
chromosome4 21414 4 1
chromosome1 50000 41 51
chromosome2 20000 1 20
chromosome3 41444 2 11
chromosome6 12141 12 22
chromosome1 50000 11 2
chromosome2 20000 3 22
chromosome3 41444 2 15
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