GSR: Simulator - srv

Basic Package Attributes
AttributeValue
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 6 years, 9 months ago
Homepagehttps://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
Documentation
Application
Support

Last evaluated07-16-2018 (824 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Sex Chromosomes,
VariationsBiallelic Marker,
Simulation MethodForward-time,
Input
Data TypeOther (Starting population (optional)),
File format
Output
Data TypeGenotype or Sequence, Mutation (Including age), Fitness,
Sequencing Reads
File FormatProgram Specific,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck, User Defined,
Gene FlowIsland Models,
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating,
FecundityConstant Number,
Natural Selection
DeterminantMulti-locus,
ModelsMulti-locus models, Random Fitness Effects,
RecombinationUniform,
Mutation ModelsInfinite-sites Model, Others (Finite-sites model),
Events AllowedPopulation Merge and Split,
Other
InterfaceCommand-line, Graphical User Interface, Script-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix, Solaris,
LanguagePython (Simupop),
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Support,

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]


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