HAPGEN protocols

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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 in pipelines

PMCID: 4856879
PMID: 26839038
DOI: 10.1038/ejhg.2016.1

[…] african samples)., sets of six cohorts were meta-analysed across five loci under various allelic heterogeneity models and ancestry compositions of the contributing cohorts. data were simulated using hapgen2 from 6 populations based on the 1000 genomes june 2011 haplotypes: ceu, tsi (european reference panels (rps)), chb, jpt (east asian rps), lwk, and yri (african rps). each cohort was composed […]

PMCID: 4583479
PMID: 26406328
DOI: 10.1371/journal.pgen.1005535

[…] causal variants in a region, 1000 regions containing two distinct variants (ceu r 2<0.05) with a maf~10% in the central 750kb of the 1mb interval were selected. haplotypes were simulated using hapgen2 with, with each of the two variants assigned an additive phenotypic effect (or = 1.2). for each raf/or parameter setting, genotypes were generated for ten “studies” of 1,000 cases and 1,000 […]

PMCID: 3559437
PMID: 23383238
DOI: 10.1371/journal.pone.0055600

[…] mach: http://www.sph.umich.edu/csg/abecasis/mach/download/, impute2: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html, beagle: http://faculty.washington.edu/browning/beagle/beagle.html, hapgen2: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html, hapmap3: http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2009-02_phaseiii/hapmap3 r2/, 1000 genomes: […]

PMCID: 3384355
PMID: 22754564
DOI: 10.3389/fgene.2012.00117

[…] autosomal chromosome using the 1kgp panel for latinos. therefore, our results serve as a guide to future imputation based analysis in latinos., the urls for data presented herein are as follows:, hapgen, https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html, impute, https://mathgen.stats.ox.ac.uk/impute/impute_v1.html#using_impute_with_the_hapmap_data, eigensoft, […]

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HAPGEN in publications

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 […]

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 […]

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, […]

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 […]

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 […]

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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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