SimuFamily

Simulation for nuclear family

---

This procedure helps generate nuclear families, having two parents and a pair of children.

**Subcommand: **
simufam

Available Options
-f, --num-fam <arg>
Specify the number of families.</arg>

-m, --num-marker <arg>
Specify the number of markers.</arg>

-s, --seed <arg>
Specify the seed of random number generator.</arg>

--make-bed
If this option is set, then .bed, .bim and .fam files will be outputted; otherwise .ped and .map files will be outputted.

--out <arg>
Specify the output root filename</arg>

--freq <arg>
Specify the allelic frequency for simulation. By default, freq = 0.5 for all loci.</arg>

--unif-freq
Randomly generate allelic frequency in a uniform distribution from 0.01 to 0.5.

--rec <arg>
Specify a universal recombination fraction, which is applied to the genome.</arg>

--rec-sex <arg>
Specify a universal recombination fractions for males and females.</arg>

--unif-rec
Randomly generate recombination fractions in a uniform distribution from 0 to 0.5.

--ld <arg>
Specify a universal ld (in DPrime). By defaulty, ld = 0.</arg>

--rand-ld
Generates ld from the uniform distribution from -1 to 1.

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
~~~~~~~~~~