From tbiltonmaths.otago.ac.nz Wed Jul 12 23:51:58 2017
From: Timothy Bilton <tbiltonmaths.otago.ac.nz>
Subject: Phasing in CRIMAP for fullsib families
Date: Thu, 13 Jul 2017 16:51:52 +1200
To: CriMap Users <crimapusersanimalgenome.org>
ReturnPath: <tbiltonmaths.otago.ac.nz>
Hi There,
I have a question regarding phasing in CRIMAP for fullsib families.
I have been using CRIMAP to estimate recombination fractions for a
fullsib family using the "fixed" command, where I know the order of the
loci. Someone told me that CRIMAP outputs the phase in the parents,
whereas I thought that since CRIMAP is an implementation of the
landergreen HMM (I'm assuming that is correct) that it does not need to
infer the phase in the parents before estimating the rf's.
It would be much appreciated if someone could clarify what CRIMAP does
in this regard.
Thanks,
Timothy Bilton

Ph.D. Candidate
Department of Mathematics and Statistics
University of Otago
P.O. Box 56
Dunedin 9054
New Zealand
Email: tbiltonmaths.otago.ac.nz
Homepage: https://www.stats.otago.ac.nz/?postgraduates=timothy_bilton
