QMSim - CGIL - University of Guelph

INPUT PARAMETER FILE
The program requires a parameter file, in which various parameters for the simulation should be
specified. The parameter file consists of five main sections. The first part describes global
parameters, the second part describes historical generations, the third part describes parameters for
subpopulations and generations, the fourth part contains genome parameters and the fifth part is
related to the output options. The order of commands within each section is not normally important.
An example of parameter file is given below.
/*******************************
** Global parameters **
*******************************/
title = "Simulating two divergent lines - 50k SNP panel";
nr = 1; //Number of replicates
h2 = 0.2; //Overall heritability
qtlh2 = 0.2; //QTL heritability
phvar = 1.0; //Phenotypic variance
/*******************************
** Historical generations **
*******************************/
begin_hist; //Historical generations
nhg = 200; //Number of historical generations
sfhg = 420; //Size of the first historical generation
sihg = 420; //Size of intermediate historical generation
ihg = 200; //Intermediate historical generation number
slhg = 420; //Size of the last historical generation
nmlhg = 20; //Number of male in the last historical generation
end_hist;
/*******************************
** Populations **
*******************************/
begin_pop = "Line 1";
begin_founder;
male [n = 20, pop = "hp"];
female [n = 400, pop = "hp"];
end_founder;
ls = 1 2 [0.05]; //Litter size
pmp = 0.5 /fix; //Proportion of male progeny (random, fix or fixwf)
ng = 10; //Number of generations
md = random; //Mating design
sr = 0.4; //Replacement ratio for sires
dr = 0.2; //Replacement ratio for dams
sd = phenotypic /h; //Selection design
cd = age; //Culling design
begin_popoutput;
ld /bin 10 /maf 0.1 /gen 0;
data;
genotype /snp_code;
allele_freq /gen 10;
end_popoutput;
end_pop;
begin_pop = "Line 2";
Dairy Cattle Breeding and Genetics Committee Meeting, September 18, 2008. 4