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GSR: Simulator - HAPGEN
| Attribute | Value |
|---|---|
| Title | HAPGEN |
| Short Description | A simulator for the simulation of case control datasets at SNP markers |
| Long Description | 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. |
| Version | 2.1.2 |
| Project Started | 2010 |
| Last Release | 13 years, 5 months ago |
| Homepage | https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html  |
| Citations | Su Z, Marchini J, Donnelly P, HAPGEN2: simulation of multiple disease SNPs., Bioinformatics, Aug. 15, 2011 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Oct. 17, 2019 (1973 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers |
| Variations | Biallelic Marker |
| Simulation Method | Resample Existing Data |
| Input | |
| Data Type | Empirical (Hapmap 3 or 1000 genomes), Other (Disease model) |
| File format | Other (Impute) |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | Other (Used by impute, impute2, snptest and gtool. ) |
| Sample Type | Case-control |
| Phenotype | |
| Trait Type | |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix |
| Language | C or C++, R |
| License | Other (Property of the university of oxford, for academic use only) |
| GSR Certification | Documentation, Application |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used HAPGEN.
2023
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, July 9, 2023 [Abstract]
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, Feb. 14, 2023 [Abstract]