I'm attempting to use PhaseByTransmission
Ah, I was wondering if a question was forthcoming... not that I'm complaining, that was a very straightforward statement, and easy to address.
As for the author of PBT -- I believe it was originally written by Menachem Fromer, who is now at Mount Sinai Hospital in NYC. He has a forum section here for his XHMM tool, if you want to try to contact him that way: http://gatkforums.broadinstitute.org/categories/xhmm
I am attempting to use PhaseByTransmission
I'd like to discuss the use of multiallelic variants with the authors, so I'm just looking for their contact information.
Correction -- PBT was actually written by Laurent Francioli. I have notified him of your interest and invited him to respond in this thread.
I indeed wrote PBT and currently it doesn't support multi-allelic sites. I am however planning to address this in the next few months.. If you have ideas or want to help with it, I'd of course be happy to hear your suggestions!
Do you have a written description of the algorithm available? This might help me see how I could help.