Simulate genotypes for SNPs, considering MAF and LD structure
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3.3 years ago
J.F.Jiang ▴ 860

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 • 1.3k views
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2.4 years ago
Shicheng Guo ★ 8.6k

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

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

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