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GSR: Simulator - srv
| Attribute | Value |
|---|---|
| Title | srv |
| Short Description | Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. |
| Long Description | srv simulates the introduction and evolution of genetic variants in one or more regions of chromosomes. These regions span roughly 10k to 100k basepair and can be considered as a gene. During evolution, mutants are introduced to the population and change the fitness of individuals who carry these mutants. The most distinguishing feature of this script is that it allows multi-locus fitness schemes with random or locus-specific diploid single-locus selection models to newly arising mutants. A multi-locus selection model is used to assign a fitness value to individuals according the mutants they carry. |
| Version | 1.3 |
| Project Started | 2011 |
| Last Release | 11 years, 9 months ago |
| Homepage | https://github.com/BoPeng/simuPOP-examples/tree/master/published/simuRareVariants |
| Citations | Peng B, Liu X, Simulating sequences of the human genome with rare variants., Hum Hered, Jan. 1, 2010 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | July 16, 2018 (2616 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Sex Chromosomes, |
| Variations | Biallelic Marker, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Other (Starting population (optional)), |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Mutation (Including age), Fitness, |
| Sequencing Reads | |
| File Format | Program Specific, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck, User Defined, |
| Gene Flow | Island Models, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, |
| Fecundity | Constant Number, |
| Natural Selection | |
| Determinant | Multi-locus, |
| Models | Multi-locus models, Random Fitness Effects, |
| Recombination | Uniform, |
| Mutation Models | Infinite-sites Model, Others (Finite-sites model), |
| Events Allowed | Population Merge and Split, |
| 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: 1
The following 1 publications are selected examples of applications that used srv.
2012
Cheung YH, Wang G, Leal SM, Wang S, A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders., Genet Epidemiol, Nov. 1, 2012 [Abstract]