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Does WISECONDOR ... ?
No, I tried and I believe that the extremely low amount of reads used for WISECONDOR does not provide enough information to identify the fetal fraction reliably. I know some other methods that try to determine this fraction, but as far as I have tested them, none seem to work reliable with such low amounts of reads.
No, right now, WISECONDOR completely ignores non-autosomal chromosomes. Some extensions to WISECONDOR did show some promising results that might be looked into further, but for now, this is it.
No, I did come up with a method to do this but it was not merged into WISECONDOR yet. Again, WISECONDOR ignores non-autosomal chromosomes.
Try this first, then ask: Simple Answers
If you run into issues, please create a ticket so I can take care of it.
If you have other troubles running WISECONDOR or any related questions, feel free to contact me through the e-mail adress on my GitHub page.