Ok, I think I get it. Instead of $data{HG00553}[162] pointing to an array of two-bit elements as I did, you want it to contain a comma-delimited string of those elements? In that case, you can join them together after the array is built by inserting this line into my code:

$data{HG00553}[162] = join ',', @{$data{HG00553}[162]};
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That still leaves the question of what you'd want in any undefined elements of the array, though.