QTPolygenicSimu

Simulation for polygenic quantitative traits

Master option
simuqt

Options
--sample-size/--n
Specify the sample size. 100 by default.

--marker/--m
Specify the number of total markers. 100 by default.

--null-marker
Specify the number of markers from null distribution. 0 by default.

--freq <arg></arg>
Specify the frequencies for the markers. 0.5 by default.

--unif-freq
It generates frequency spectrum from uniform distribution between 0.01~0.5.

--freq-file
Specify the file which contains frequency for the reference alleles. One element per line.

--poly-effect
It generates polygenic effects from the standard normal distribution.

--poly-effect-sort
It generates polygenic effects from the standard normal distribution. Different from --poly-effect, this option will sort the genetic effects in ascending order to the markers, say the first marker has the smallest effect and the last the biggest.

--effect <arg>
Specify the universal effect of each loci. 0.5 by default.</arg>

--effect-file <arg>
Specify the file which contains the effects for each locus.</arg>

--ld <arg>
Specify LD in Lewontin's D', a value between -1 to 1. 0 by default.</arg>

--rand-ld
It generates Lewontin's D' from the uniform distribution between -1,1.

--hsq <arg>
Specify the heritability. 0.5 by default.</arg>

--make-bed
It generates genotypes in bed format.

Examples

gear simuqt --n 1000 --m 1000 --null-loci 900 --freq 0.45 --ld 0.3 --hsq 0.25 --poly-effect --out test
gear simuqt --n 1000 --m 1000 --null-loci 500 --unif-freq --rand-ld --hsq 0.2 --effect-file eff.txt --out test
gear simuqt --n 1000 --m 1000 --freq-file frq.txt --poly-effect --ld 0.8 --out test

The output files includes
.phe: there are four columns included. The first two columns are family id, and individual id. The 3rd column is genotypic values (breeding values), and the 4th column is phenotypic values.
.rnd: there are three columns included. 1st is the marker name, 2nd is the reference alleles, the 3rd column is additive effects.
.add: the genotype in additive model coding scheme.
.bim, .fam, .bed: the genotype in plink binary format.