From tbiltonmaths.otago.ac.nz  Wed Jul 12 23:51:58 2017
From: Timothy Bilton <tbiltonmaths.otago.ac.nz>
Subject: Phasing in CRI-MAP for full-sib families
Date: Thu, 13 Jul 2017 16:51:52 +1200
To: Cri-Map Users <crimap-usersanimalgenome.org>
Return-Path: <tbiltonmaths.otago.ac.nz>

Hi There,

I have a question regarding phasing in CRI-MAP for full-sib families.

I have been using CRI-MAP to estimate recombination fractions for a 
full-sib family using the "fixed" command, where I know the order of the 
loci. Someone told me that CRI-MAP outputs the phase in the parents, 
whereas I thought that since CRI-MAP is an implementation of the 
lander-green 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 CRI-MAP 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