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GSR: Simulator - simuGWAS
| Attribute | Value |
|---|---|
| Title | simuGWAS |
| Short Description | A forward-time simulator that simulates realistic samples for genome-wide association studies. |
| Long Description | simuGWAS evolves a population forward in time, subject to rapid population expansion, mutation, recombination and natural selection. A trajectory simulation method is used to control the allele frequency of optional disease predisposing loci. A scaling approach can be used to improve efficiency when weak, additive genetic factors are used. |
| Version | 1.0 |
| Project Started | 2009 |
| Last Release | 15 years ago |
| Homepage | https://github.com/BoPeng/simuPOP-examples/tree/master/published/simuGWAS |
| Citations | Peng B, Amos CI, Forward-time simulation of realistic samples for genome-wide association studies., BMC Bioinformatics, Sept. 1, 2010 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | March 28, 2020 (1995 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, |
| Variations | Biallelic Marker, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Empirical (Hapmap 2 or 3), Other (List of markers (optional)), |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, |
| Sequencing Reads | |
| File Format | Program Specific (A simupop population), |
| Sample Type | Random or Independent, Sibpairs, Trios and Nuclear Families, Case-control, |
| Phenotype | |
| Trait Type | |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, |
| Gene Flow | Stepping Stone Models, Admixed Population, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, |
| Fecundity | Constant Number, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, |
| Recombination | Uniform (Proportional to marker distance), |
| Mutation Models | Two-allele Mutation Model, |
| Events Allowed | |
| Other | |
| Interface | Command-line, Graphical User Interface, Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
| Language | Python (Simupop), |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 6
The following 6 publications are selected examples of applications that used simuGWAS.
2019
Dimitromanolakis A, Paterson AD, Sun L, Fast and Accurate Shared Segment Detection and Relatedness Estimation in Un-phased Genetic Data via TRUFFLE., Am J Hum Genet, July 3, 2019 [Abstract]
Dimitromanolakis A, Paterson AD, Sun L, Fast and Accurate Shared Segment Detection and Relatedness Estimation in Un-phased Genetic Data via TRUFFLE., Am J Hum Genet, July 3, 2019 [Abstract]
2013
Sim A, Tsagkrasoulis D, Montana G, Random forests on distance matrices for imaging genetics studies., Stat Appl Genet Mol Biol, Dec. 1, 2013 [Abstract]
2012
Brown MD, Glazner CG, Zheng C, Thompson EA, Inferring coancestry in population samples in the presence of linkage disequilibrium., Genetics, April 1, 2012 [Abstract]
Wang Y, Gjuvsland AB, Vik JO, Smith NP, Hunter PJ, Omholt SW, Parameters in dynamic models of complex traits are containers of missing heritability., PLoS Comput Biol, Jan. 1, 2012 [Abstract]
Bouaziz M, Paccard C, Guedj M, Ambroise C, SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies., PLoS One, Jan. 1, 2012 [Abstract]