Question: Simulate genotypes based on reference genotypes with same LD structure?
1
gravatar for Veera
2.3 years ago by
Veera 90
Denmark
Veera 90 wrote:

If I have whole genome genotypes of, for example, 10,000 samples as reference data. Is it possible to simulate a gwas data (100 samples) with exactly the same LD structure as my reference gwas data ?

genotype ld plink simulate • 950 views
ADD COMMENTlink modified 6 months ago by Shicheng Guo7.5k • written 2.3 years ago by Veera 90
2
gravatar for Shicheng Guo
6 months ago by
Shicheng Guo7.5k
Shicheng Guo7.5k wrote:

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

ADD COMMENTlink written 6 months ago by Shicheng Guo7.5k

It would be nice to have links, too.

ADD REPLYlink written 6 months ago by zx87547.5k
1
gravatar for Petr Ponomarenko
2.3 years ago by
United States / Los Angeles / ALAPY.com
Petr Ponomarenko2.6k wrote:

Yes. There are many tools:

  • simuPOP is quite popular for population simulations
ADD COMMENTlink modified 6 months ago by zx87547.5k • written 2.3 years ago by Petr Ponomarenko2.6k
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