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 | 9 years, 6 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, 08-15-2011 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 10-17-2019 (552 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, |
No example publication using HAPGEN has been provided.
Please propose new citations if you are aware of publications that use this software.