HAPGEN statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HAPGEN

Tool usage distribution map

This map represents all the scientific publications referring to HAPGEN per scientific context
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Associated diseases

This word cloud represents HAPGEN usage per disease context

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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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