Basic Package AttributesAttribute | Value |
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Title | HAPGEN |
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Short Description | A simulator for the simulation of case control datasets at SNP markers |
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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.
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Version | 2.1.2 |
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Project Started | 2010 |
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Last Release | 8 years, 1 month ago |
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Homepage | https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html |
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Citations |
Su Z, Marchini J, Donnelly P, HAPGEN2: simulation of multiple disease SNPs., Bioinformatics, Aug. 15, 2011
[Abstract, cited in
PMC
]
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GSR Certification | Accessibility ✔Documentation Application Support
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Last evaluated | Oct. 17, 2019 (34 days ago) |
Recently certified
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. |
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Detailed AttributesAttribute Category | Attribute | Target | |
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Type of Simulated Data | Genotype at Genetic Markers,
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Variations | Biallelic Marker,
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Simulation Method | Resample Existing Data,
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Input | |
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Data Type | Empirical (Hapmap 3 or 1000 genomes),
Other (Disease model),
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File format | Other (Impute),
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Output | |
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Data Type | |
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Sequencing Reads | |
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File Format | Other (Used by impute, impute2, snptest and gtool. ),
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Sample Type | Case-control,
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Phenotype | |
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Trait Type | |
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Determinants | Single Genetic Marker,
Multiple Genetic Markers,
Gene-Gene Interaction,
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Evolutionary Features | |
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Demographic | |
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Population Size Changes | |
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Gene Flow | |
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Spatiality | |
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Life Cycle | |
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Mating System | |
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Fecundity | |
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Natural Selection | |
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Determinant | |
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Models | |
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Recombination | |
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Mutation Models | |
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Events Allowed | |
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Other | |
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Interface | Command-line,
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Development | |
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Tested Platforms | Mac OS X,
Linux and Unix,
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Language | C or C++,
R,
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License | Other (Property of the university of oxford, for academic use only),
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GSR Certification | Documentation,
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No example publication using HAPGEN has been provided.
Please
propose new citations if you are aware of publications that use this software.