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Simulate genotypes based on reference genotypes with same LD structure?

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
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updated by Shicheng Guo Shicheng Guo • written by Veera Veera

2 answers

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

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written by Shicheng Guo Shicheng Guo

It would be nice to have links, too.

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written by zx8754 zx8754

Yes. There are many tools:

  • simuPOP is quite popular for population simulations
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updated by zx8754 zx8754 • written by Petr Ponomarenko Petr Ponomarenko

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