Simulate genotypes for SNPs, considering MAF and LD structure

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

genotype simulation snp maf ld

• 2,925 views • link

updated 7.7 years ago by zx8754

• written 8.6 years ago by J.F.Jiang

Simulate genotypes based on reference genotypes with same LD structure?

• 0 views • link

written 7.7 years ago by zx8754

1 answer

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

• 0 views • link

written 7.7 years ago by Shicheng Guo

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

• 0 views • link

written 7.7 years ago by zx8754

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