HAPGEN protocols

HAPGEN specifications

Information


Unique identifier OMICS_04379
Name HAPGEN
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

 (6)
2016
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 hapgen212 from 6 populations based on the 1000 genomes june 2011 haplotypes:13 ceu, tsi (european reference panels (rps)), chb, jpt (east asian rps), lwk, and yri (african rps). each cohort […]

2015
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 […]

2013
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: […]

2013
PMCID: 3559437
PMID: 23383238
DOI: 10.1371/journal.pone.0055600

[…] 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: […]

2013
PMCID: 3559437
PMID: 23383238
DOI: 10.1371/journal.pone.0055600

[…] 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: […]

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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