Assuming the data is in $hash.

while (my ($key1, $data1) = each %$hash) {
    while (my ($key2, $data2) = each %$data1) {
       printf "%s,%s-\nRCC,%s,T,T,C,CA,GT,T,GA,C,A,G,CT," .
              "T,T,CA,AG,TC,G,GA,C,TC,CT,AG,AG,C,GT,GA,G," .
              "GA,T", $$data2{plex}, $key1, $$data2{gt};
    }
}
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