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 | 9 years, 3 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, 01-01-2015 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 11-05-2020 (1255 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.