Simulate genotypes for SNPs, considering MAF and LD structure

Question

[J.F.Jiang]

Hi all,

I want to simulate genotypes of several SNPs for 10,000 samples.

A Bernoulli sampling is applied to generate SNP genotypes (0/0, 0/1, 1/1) for random samples.

However, this will not consier the LD structure among thse SNPs, which was obtained from 1KG dataset.

Is there any tools of Github project that I can apply to simulate these SNPs' genotypes?

Best,

Junfeng

[zx8754]

Related post:

• Simulate genotypes based on reference genotypes with same LD structure?

Answer 1

[Shicheng Guo]

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

[zx8754]

No need to repeat the answer, just add a link as a comment. (as I just did, see above)