Question

Simulate genotypes based on reference genotypes with same LD structure?

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7.2 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 • 2.5k views

ADD COMMENT • link updated 5.4 years ago by Shicheng Guo ★ 9.4k • written 7.2 years ago by Veera ▴ 90

score 2 · Answer 1 · 2018-11-19

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5.4 years ago

Shicheng Guo ★ 9.4k

Simple bi-allelic SNPs without structure: PLINK

Coalescent approaches: GENOME

Forward-time approaches: MetaSim and simuPop

Resampling approaches: Hapgen2

ADD COMMENT • link 5.4 years ago by Shicheng Guo ★ 9.4k

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It would be nice to have links, too.

ADD REPLY • link 5.4 years ago by zx8754 11k

zx8754 · Answer 2 · 2017-02-22

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7.2 years ago

Petr Ponomarenko ★ 2.8k

Yes. There are many tools:

simuPOP is quite popular for population simulations

ADD COMMENT • link updated 5.4 years ago by zx8754 11k • written 7.2 years ago by Petr Ponomarenko ★ 2.8k