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 | 13 years, 6 months 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, 09-01-2010 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 03-28-2020 (1477 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, 07-03-2019 [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, 07-03-2019 [Abstract]
2013
Sim A, Tsagkrasoulis D, Montana G, Random forests on distance matrices for imaging genetics studies., Stat Appl Genet Mol Biol, 12-01-2013 [Abstract]
2012
Brown MD, Glazner CG, Zheng C, Thompson EA, Inferring coancestry in population samples in the presence of linkage disequilibrium., Genetics, 04-01-2012 [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, 01-01-2012 [Abstract]
Bouaziz M, Paccard C, Guedj M, Ambroise C, SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies., PLoS One, 01-01-2012 [Abstract]