Question: Rare Variant Simulation
gravatar for cbm
8.0 years ago by
cbm20 wrote:

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.

simulation variant • 1.9k views
ADD COMMENTlink written 8.0 years ago by cbm20

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.

ADD REPLYlink written 8.0 years ago by Zev.Kronenberg11k

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!

ADD REPLYlink written 7.9 years ago by cbm20
gravatar for Kevin
8.0 years ago by
Kevin630 wrote:

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

ADD COMMENTlink written 8.0 years ago by Kevin630
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