I'm not sure why you're building up @chrnums and @coords and then taking a slice of @twodarray. You should be able to do everything in 1 step with something like:

my @data = ( [ 'chr1', 10 ],
             [ 'chr1', 30 ],
             [ 'chr1', 20 ],
             [ 'chr3', 11 ],
             [ 'chr3', 40 ],
             [ 'chr2', 10 ],
             [ 'chr3', 10 ],
             [ 'chr2', 40 ],
             [ 'chr3', 20 ],
             [ 'chr2', 20 ],
           );

my @sorted = sort { $a->[0] cmp $b->[0]
                    ||
                    $a->[1] <=> $b->[1]
                  } @data
             ;
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