Question: Simulate genotypes for SNPs, considering MAF and LD structure
0
gravatar for J.F.Jiang
13 months ago by
J.F.Jiang730
China
J.F.Jiang730 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 • 572 views
ADD COMMENTlink modified 12 weeks ago by zx87546.5k • written 13 months ago by J.F.Jiang730

Related post:

ADD REPLYlink written 12 weeks ago by zx87546.5k
2
gravatar for Shicheng Guo
12 weeks ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

ADD COMMENTlink written 12 weeks ago by Shicheng Guo7.4k
1

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

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by zx87546.5k
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