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 | 10 years, 3 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, 01-01-2010 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 07-16-2018 (2098 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, 11-01-2012 [Abstract]