GSR: Simulator - HAPGEN

Basic Package Attributes
AttributeValue
Title HAPGEN
Short Description A simulator for the simulation of case control datasets at SNP markers
Long Description HAPGEN2 is a an updated version of the program HAPGEN, which simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs. We hope to add further facilities to simulate quantitive traits and admixture soon.
Version 2.1.2
Project Started 2010
Last Release 9 years ago
Homepagehttps://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
Citations Su Z, Marchini J, Donnelly P, HAPGEN2: simulation of multiple disease SNPs., Bioinformatics, 08-15-2011 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated10-17-2019 (366 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 DataGenotype at Genetic Markers,
VariationsBiallelic Marker,
Simulation MethodResample Existing Data,
Input
Data TypeEmpirical (Hapmap 3 or 1000 genomes), Other (Disease model),
File formatOther (Impute),
Output
Data Type
Sequencing Reads
File FormatOther (Used by impute, impute2, snptest and gtool. ),
Sample TypeCase-control,
Phenotype
Trait Type
DeterminantsSingle Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction,
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++, R,
LicenseOther (Property of the university of oxford, for academic use only),
GSR CertificationDocumentation,

No example publication using HAPGEN has been provided.

Please propose new citations if you are aware of publications that use this software.


Propose changes to this simulator