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HAPGEN specifications


Unique identifier OMICS_04379
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Programming languages C++, R
Computer skills Advanced
Version 2.2.0
Stability Stable
Maintained Yes




No version available

Publication for HAPGEN

HAPGEN citations


A method combining a random forest based technique with the modeling of linkage disequilibrium through latent variables, to run multilocus genome wide association studies

BMC Bioinformatics
PMCID: 5870262
PMID: 29587628
DOI: 10.1186/s12859-018-2054-0
call_split See protocol

[…] To simulate realistic genotypic data and an association between one of these SNPs and the disease status, we relied on one of the most widely-used software programs, HAPGEN (http://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html) []. To control the effect size of the causal SNPs, three ingredients were combined: severity of the disease expressed as ge […]


Determining Genetic Causal Variants Through Multivariate Regression Using Mixture Model Penalty

Front Genet
PMCID: 5844985
PMID: 29556250
DOI: 10.3389/fgene.2018.00077
call_split See protocol

[…] Hapgen2 (Su et al., ) and 1,000 Genomes (1000 Genomes Project Consortium et al., ) is used for simulating realistic genotypes for an European population of size 100,000 considering all the 22 chromoso […]


cophesim: a comprehensive phenotype simulator for testing novel association methods

PMCID: 5605948
PMID: 28979766
DOI: 10.5256/f1000research.12938.r24718

[…] One solution is to use artificial data simulated with specific assumptions.The best existing phenotype simulators, such as: GENOME , Plink , phenosim , CoaSim , Fregene , ForSim , QuantiNemo , GCTA , HapGen , SeqSimla , and SimRare offer qualitative and dichotomous simulated phenotype. But the known phenotype simulation software tools have some limitations, which may prevent customers from using […]


Trans ethnic meta regression of genome wide association studies accounting for ancestry increases power for discovery and improves fine mapping resolution

Hum Mol Genet
PMCID: 5755684
PMID: 28911207
DOI: 10.1093/hmg/ddx280
call_split See protocol

[…] ed at random from those reported in the reference panel from Phase 3 of the 1000 Genomes Project () with MAF > 1% in all reference populations. Genotypes in each population were then simulated, using HAPGEN2 (), using the causal variant population-specific odds-ratio () and haplotypes from the 1000 Genomes Project Phase 3 reference panel ().We first considered the ‘perfect’ data setting, where all […]


Pathway Based Kernel Boosting for the Analysis of Genome Wide Association Studies

PMCID: 5530424
PMID: 28785300
DOI: 10.1155/2017/6742763

[…] lting in a realistic correlation structure for all simulation scenarios. In each of the 100 simulation runs, new genotype data for a total of 11,665 SNPs in 2,333 pseudogenes were simulated using the HAPGEN2 software. This software generates new haplotype data by combining a given set of reference haplotypes with previously simulated data. The detailed procedure is described in [].In the null case […]


Simulating Next Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

PLoS One
PMCID: 5125660
PMID: 27893777
DOI: 10.1371/journal.pone.0167047

[…] lly simulate events such as linkage disequilibrium or other population-level genetics information. To simulate this type of data, known variants can be introduced using the VCF file, or tools such as HAPGEN2 [] can be used to simulate disease SNPs that can be subsequently introduced into NEAT reads. […]


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HAPGEN institution(s)
Wellcome Trust Centre for Human Genetics, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK
HAPGEN funding source(s)
Supported by Wellcome Trust grants 084575/Z/08/Zand075491/Z/04/B, a Wolfson Royal Society Merit Award and by United Kingdom Medical Research Council grant number G0801823.

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