Experimental population - gc5k/GEAR GitHub Wiki
###Simulation for experimental population### Four experimental populations are considered: Backcross population (bc), F2 (f2), double-haploid (dh), recombinant inbred lines (ril), and immortalized F2 (if2).
Mast command: labpop
Options
--bc/--dh/--f2/--ril/--if2
Simulating backcross/double haploid/f2/recombiant inbred lines/immortalized f2.
--sample-size/--n
Specify the sample size. 100 by default.
--marker/--m
Specify the number of total markers. 100 by default.
--rec
Specify the recombination fraction for marker i and maker i+1.
--rand-rec
Recombination fraction will be randomly generated from a uniform distribution between 0 and 0.5.
--rec-file
Specify the recombination fraction in the file. When m markers are simulated, this file should have m rows, one element per row. Regardless the value of the first element, it will be ignored.
--effect-file
Specify the effect for each loci; otherwise the effects will be randomly generated from the standard normal distribution.
--hsq
Specify the heritability. It defaults to 0.5.
--rep
Specify the replication for simulation. It defaults to 1.
--make-bed
It generates genotypes in bed format.
--1234-mode/--atgc-mode
The alleles will be in numeric mode if --1234-mode is specified, or alphabetic mode if --atgc-mode is specified.
--seed
Specifiy the seed for simulation.
Examples
gear labpop --bc --n 1000 --m 100 --rec 0.1 --hsq 0.25 --out test
gear labpop --dh --n 1000 --m 100 --rec-file rec.txt --hsq 0.25 --out test
gear labpop --f2 --n 500 --m 100 --rec 0.2 --make-bed --out test
gear labpop --ril --n 500 --m 100 --rec-file rec.txt --seed 2016 --out test
gear labpop --if2 --n 500 --m 100 --rec-file rec.txt --seed 2016 --out test
The output files includes *.bim, *.fam, and *.bed (the genotype file in plink binary format). When --make-bed is not specified, the genotypes are in ped and map format.
*.phe: there are three columns included. The first two columns are family id, and individual id. The 3rd column is a phenotypic value. When replication is bigger than 1, from the 4th column represents phenotypic values for each replication.
*.breed: there are three columns included. The first two columns are family id, and individual id. The 3rd column is genotypic value (breeding value).