That doesn't make any sense, HL. You're not performing any uniquification operations. There should at least be a `uniq` before you redirect the output to `UNIQFILE`.
You either need to apply `uniq` directly to the data lines in the VCF file or you need to apply it to a subset of the columns. What you're doing here will just recreate the file after taking a few detours that do a bunch of stuff serving no purpose.