Simulate genotypes based on reference genotypes with same LD structure?
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4.1 years ago
Veera ▴ 90

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 ?

plink simulate genotype ld • 1.6k 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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It would be nice to have links, too.

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4.1 years ago

Yes. There are many tools:

  • simuPOP is quite popular for population simulations
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