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GSR: Simulator - Variant Simulation Tools
| Attribute | Value |
|---|---|
| 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 | 10 years, 9 months ago |
| Homepage | http://varianttools.sourceforge.net/Simulation/HomePage |
| Citations | Peng B, Reproducible simulations of realistic samples for next-generation sequencing studies using variant simulation tools., Genet Epidemiol, Jan. 1, 2015 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Nov. 5, 2020 (1773 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | VCF, |
| Sample Type | Random or Independent, Sibpairs, Trios and Nuclear Families, Case-control, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, |
| Determinants | Multiple Genetic Markers, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | Stepping 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 System | Random Mating, Selfing, |
| Fecundity | |
| Natural Selection | |
| Determinant | Multi-locus, |
| Models | Other, |
| Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
| Mutation Models | Two-allele Mutation Model, k-Allele Model, Codon and Amino Acid Models, |
| Events Allowed | Population Merge and Split, Varying Genetic Features, Change of Mating Systems, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | C or C++, Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using Variant Simulation Tools has been provided.
Please propose new citations if you are aware of publications that use this software.