A two hash approach:

my ( @hashes ) = ({},{});
while(<>) {
    chomp;
    @_=split /\,/;
    $hashes[$_]{$_[$_]} = 1 for (0..1);
}
@_=sort keys %{$hashes[1]};
print "$_," . shift(@_) . "\n" for sort keys %{$hashes[0]}
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