Question: Simulate genotypes for SNPs, considering MAF and LD structure
0
gravatar for J.F.Jiang
11 months ago by
J.F.Jiang720
China
J.F.Jiang720 wrote:

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

ld genotype snp simulation maf • 480 views
ADD COMMENTlink modified 28 days ago by zx87546.1k • written 11 months ago by J.F.Jiang720

Related post:

ADD REPLYlink written 28 days ago by zx87546.1k
2
gravatar for Shicheng Guo
28 days ago by
Shicheng Guo7.3k
Shicheng Guo7.3k wrote:

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

ADD COMMENTlink written 28 days ago by Shicheng Guo7.3k
1

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

ADD REPLYlink modified 28 days ago • written 28 days ago by zx87546.1k
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