Genotype simulation using allele frequencies and LD

[KangchengHou]

use HapSim (https://academic.oup.com/bioinformatics/article/21/23/4309/194848) and simulate recombination events so that we can simulate admixed individual with only LD matrices (without large number of individual haplotype data)

[KangchengHou]

simple experiment with this hapsim package is performed, however, that implementation seems to be work with > 50 SNPs. A wrapper of hapgen2 has been added. So the current preferred approach is to first simulate some haplotypes with hapgen2 and then simulate the cross-over process.