QTL analysis

From: Agus Susanto <asusanto_at_UOGUELPH.CA>
Date: Wed, 20 Sep 2006 16:54:16 -0400

I am running an animal model with animal, permanent environment and qtl
as random effects for a trait observed only on females. I provide
var(cov)iance matrix for qtl effect with ginv.giv file with the
dimension of 8x8.
The pedigree file (ped.dat) ,for example:
1 0 0
2 0 0
3 0 0
4 1 2
5 3 2
6 1 5
7 3 4
8 1 7

and the data file (tes.dat), for example:
cow sire dam parity hys pe fat
4 1 2 1 1 4 4 201
4 1 2 2 3 4 4 280
5 3 2 1 1 5 5 150
5 3 2 2 4 5 5 200
6 1 5 1 2 6 6 160
6 1 5 2 3 6 6 190
7 3 4 1 1 7 7 180
7 3 4 2 3 7 7 250
8 1 7 1 2 8 8 285
8 1 7 2 4 8 8 300

My control file is like this:
Single Trait Genetic Analysis with QTL>>>>>>>>>>>>>
 animal !P
 sire !P
 dam !P
 parity !I
 hys !I
 pe !I
 qtl !P #------------> is this line correct ????
 fat
ped.dat !MAKE
ginv.giv
tes.dat !MAXIT 10

fat ~ mu hys parity !r animal pe qtl

1 1 3
0 0 0

animal 1
animal 0 AINV 3.0

pe 1
pe 0 IDEN 1.5

qtl 1
qtl 0 GIV1 0.5

ASREML run without giving me error message when I put qualifier !P on
the qtl. When I changed into "qtl 8" then I have a warning saying"
Fewer levels found in qtl than specified".
I don't think using !P qualifier for qtl is correct but I have no idea
what is the correct one.
Second question is what I should write for the qtl column in my data
file if I assumed only males have been genotyped for marker.

--
Agus Susanto
Department of Animal and Poultry Science
Centre for Genetic Improvement of Livestock
University of Guelph, Guelph, Ontario, Canada N1G 2W1
Rm.128, Phone (519) 824-4120 X-58353
Received on Mon Sep 20 2006 - 16:54:16 EST

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