Rare Variant Simulation
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12.3 years ago
cbm ▴ 20

Does anyone have advice on simulation methods for rare variants? I have reviewed many collapsing methods and most do not explicitly state which (if any) available method they used. It can be a relatively simple model, I just need to confidently assess Type 1 error and power of a method on about 50kb region.

variant simulation • 2.7k views
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What does rare variant simulation mean? Do you want genotypes? Do you want allele frequencies? More information is required to point you to the right software.

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Thanks for the clarification, I would like genotypes. Ideally a ped/vcf format (although these can be scripted pretty easily). It would be best if I could simulate a population and then apply causal and non causal variants to that population. I have looked pretty closely at simuPOP and GenomePop2. I am trying simuPOP out now. Just wanted to see if there was perhaps another method I have overlooked that is popular in the field. I don't have any experience with rare variant simulators before this. Thanks!

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12.3 years ago
Kevin ▴ 640

As I understand Hapgen might help with this. Haven't used it myself so can't comment more than that.

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