Simulating discordant nuclear family - gc5k/GEAR GitHub Wiki
Simulation for nuclear families
This function generates nuclear families, which have two parents and two children.
Master option: simufam
Options
--num-fam
Specify the number of families. Short command is -f.
--num-marker
Specify the number of markers. Short command is -m.
--seed
Specify the seed of random number generator. Short command is -s.
--freq
Specify the allele frequencies. It defaults to 0.5 for all loci.
--unif-freq
Generate allele frequency drawn from a uniform distribution between 0.01 to 0.5.
--rec
Specify a universal recombination fraction.
--rec-sex
Specify a universal recombination fractions separately for males and females.
--unif-rec
Generate recombination fractions drawn from a uniform distribution between 0 to 0.5.
--ld
Specify Lewontin's D' for any pair of consecutive markers. It defaults to 0, linkage equilibrium for all markers.
--rand-ld
Generate Lewontin's D' from the uniform distribution between -1 to 1.
--make-bed
It generates genotypes in bed format.
--hsq
Specify heritability. It defaults to 0.5.
--effect-file
Specify the effects for loci. If it is not specified, it will draw effects from a standard normal distribution.
--out
Specify the root name for the output files.
Examples
1 Generating 100 nuclear families, and each individual has 100 markers. Allelic frequency is 0.5 for each locus, and loci are in linkage disequilibrium
gear simufam --num-fam 100 --num-marker 100 --out poly
2 Generating 100 nuclear families, and each individual has 100 markers. Allelic frequency is 0.5, and ld for a pair of neighboring markers is 0.8, and recombination fraction is 0.1
gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec 0.1 --out poly
3 Similar to the last simulation, but parents have heterogeneous recombination fractions of 0.1 and 0.2
gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --rec-sex 0.1 0.2 --out poly
4 Recombination follows uniform distribution
gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --unif-rec --make-bed --out poly
5 Allele frequency is 0.3 for each locus
gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --freq 0.3 --make-bed --out poly
6 Allele frequency follows uniform distribution between 0.01~0.5
gear simufam --num-fam 100 --num-marker 100 --ld 0.8 --unif-freq --make-bed --out poly