A simulator for the simulation of case control datasets at SNP markers Long Description (required)
HAPGEN2 is a an updated version of the program HAPGEN, which simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs. We hope to add further facilities to simulate quantitive traits and admixture soon. https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 21653516 ],
Su Z, Marchini J, Donnelly P ,
HAPGEN2: simulation of multiple disease SNPs. ,
Bioinformatics ,
08-15-2011 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=21653516, Primary Citation
[Pubmed ID: 36711496 ],
Yuan K, Longchamps RJ, Pardinas AF, Yu M, Chen TT, Lin SC, Chen Y, Lam M, Liu R, Xia Y, et al. ,
Fine-mapping across diverse ancestries drives the discovery of putative causal variants underlying human complex traits and diseases. ,
medRxiv ,
07-09-2023 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=36711496, , Application
[Pubmed ID: 36788230 ],
Miao J, Guo H, Song G, Zhao Z, Hou L, Lu Q ,
Quantifying portable genetic effects and improving cross-ancestry genetic prediction with GWAS summary statistics. ,
Nat Commun ,
02-14-2023 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=36788230, , Application