GSR: Simulator - HAPGEN
Attribute | Value |
---|---|
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, 3 months ago |
Homepage | https://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 |
Last evaluated | 10-17-2019 (448 days ago) |
Author verification | The 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. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, |
Variations | Biallelic Marker, |
Simulation Method | Resample Existing Data, |
Input | |
Data Type | Empirical (Hapmap 3 or 1000 genomes), Other (Disease model), |
File format | Other (Impute), |
Output | |
Data Type | |
Sequencing Reads | |
File Format | Other (Used by impute, impute2, snptest and gtool. ), |
Sample Type | Case-control, |
Phenotype | |
Trait Type | |
Determinants | Single 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 | |
Interface | Command-line, |
Development | |
Tested Platforms | Mac OS X, Linux and Unix, |
Language | C or C++, R, |
License | Other (Property of the university of oxford, for academic use only), |
GSR Certification | Documentation, |
No example publication using HAPGEN has been provided.
Please propose new citations if you are aware of publications that use this software.