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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




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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

PMCID: 5870262
PMID: 29587628
DOI: 10.1186/s12859-018-2054-0

[…] of our methodological analysis., 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 […]


Determining Genetic Causal Variants Through Multivariate Regression Using Mixture Model Penalty

PMCID: 5844985
PMID: 29556250
DOI: 10.3389/fgene.2018.00077

[…] obtained are shown to be better correlated with the true effect sizes (in comparison with a few existing techniques). an increase in the positive and negative predictive value is demonstrated using hapgen2 simulated data., detection and estimation of the genetic causal variants associated with a particular phenotypic trait is one of the most challenging problems in modern day statistical […]


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

PMCID: 5755684
PMID: 28911207
DOI: 10.1093/hmg/ddx280

[…] 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, […]


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

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

[…] 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 […]


Simulating Next Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

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

[…] 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., to validate the output of neat, we performed several simulation workflows to confirm […]


A combined association test for rare variants using family and case control data

PMCID: 5133518
PMID: 27980639
DOI: 10.1186/s12919-016-0033-x

[…] available when we attempted to evaluate the statistical properties of the proposed tests, we used computer simulations to evaluate the type i error rates and power for the capl-burden and capl-skat. hapgen2 [] was used to simulate 2 sets of haplotypes in the microtubule-associated protein 4 (map4) gene based on the 1000 genomes project sequence data for the ceu (utah residents with northern […]

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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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