GSR: Simulator - Variant Simulation Tools

Basic Package Attributes
AttributeValue
Title Variant Simulation Tools
Short Description A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility.
Long Description Variant Simulation Tools is a module of Variant Tools for the simulation of genetic variants for sequencing-based genetic epidemiological studies. Although multiple simulation engines are provided, the core of VST is a novel forward-time simulation engine that simulates real nucleotide sequences of the human genome using DNA mutation models, fine-scale recombination maps, and a selection model based on amino acid changes of translated protein sequences. The design of VST allows users to easily create and distribute simulation methods and simulated datasets for a variety of applications and encourages fair comparison between statistical methods through the use of existing or reproduced simulated datasets.
Version 2.6.1
Project Started 2014
Last Release 5 years, 10 months ago
Homepagehttp://varianttools.sourceforge.net/Simulation/HomePage
Citations Peng B, Reproducible simulations of realistic samples for next-generation sequencing studies using variant simulation tools., Genet Epidemiol, 01-01-2015 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated11-05-2020 (1 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation,
Simulation MethodForward-time,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatVCF,
Sample TypeRandom or Independent, Sibpairs, Trios and Nuclear Families, Case-control,
Phenotype
Trait TypeBinary or Qualitative, Quantitative,
DeterminantsMultiple Genetic Markers,
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined,
Gene FlowStepping Stone Models, Island Models, Continent-Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, Admixed Population, User-defined Matrix, Other,
Spatiality
Life Cycle
Mating SystemRandom Mating, Selfing,
Fecundity
Natural Selection
DeterminantMulti-locus,
ModelsOther,
RecombinationUniform, Varying Recombination Rates, Gene Conversion Allowed,
Mutation ModelsTwo-allele Mutation Model, k-Allele Model, Codon and Amino Acid Models,
Events AllowedPopulation Merge and Split, Varying Genetic Features, Change of Mating Systems,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++, Python,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using Variant Simulation Tools has been provided.

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