HAPGEN

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Basic Package Attributes
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	8 years, 8 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, Aug. 15, 2011 [Abstract, cited in PMC ]
GSR Certification	Accessibility ✔Documentation Application Support
Last evaluated	Oct. 17, 2019 (249 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.

Detailed Attributes
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,