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duoHMM specifications


Unique identifier OMICS_34265
Name duoHMM
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.1.7
Stability Stable
Maintained Yes




No version available


  • person_outline Jonathan Marchini

Publication for duoHMM

duoHMM citations


Insights into Platypus Population Structure and History from Whole Genome Sequencing

Mol Biol Evol
PMCID: 5913675
PMID: 29688544
DOI: 10.1093/molbev/msy041

[…] .5 Mb, 200 conditioning states, and 30 iterations of the main MCMC, and incorporating phase-informative sequencing reads to improve phasing at rare variants (). The haplotypes were postprocessed with duoHMM (), using the two known pedigrees in the sample set to improve the phasing and correct Mendelian errors.The phased haplotypes were used to run FineSTRUCTURE (). The FineSTRUCTURE algorithm invo […]


Genome wide meta analyses of stratified depression in Generation UK and UK Biobank

PMCID: 5802463
PMID: 29317602
DOI: 10.1038/s41398-017-0034-1

[…] th a call rate of ≤98%, Hardy Weinberg Equilibrium (HWE) P-value ≤ 1 × 10−6, and a minor allele frequency (MAF) ≤ 1%. Phasing of genotype data was performed using the SHAPEIT2 algorithm utilizing the duoHMM option, which refines phasing by utilizing pedigree information. Imputation was performed using PBWT software. Multi-allelic variants, monomorphic variants and SNPs with an imputation INFO scor […]


Genome wide haplotype based association analysis of major depressive disorder in Generation UK and UK Biobank

PMCID: 5802488
PMID: 29187746
DOI: 10.1038/s41398-017-0010-9
call_split See protocol

[…] e phasing of UK Biobank was conducted on a 50 Mb window centred on those haplotypes identified within GS:SFHS with P < 10−6. The relatedness within GS:SFHS made it suitable for the application of the duoHMM method, which improves phasing accuracy by also incorporating family information. The default window size of 2 Mb was used for UK Biobank and a 5 Mb window was used for GS:SFHS as larger window […]


Haplotype based association analysis of general cognitive ability in Generation UK, the English Longitudinal Study of Ageing, and UK Biobank

Wellcome Open Res
PMCID: 5605947
PMID: 28989979
DOI: 10.21956/wellcomeopenres.13175.r25393
call_split See protocol

[…] for ELSA and UK Biobank), as this has been shown to be advantageous when larger amounts of identity by descent (IBD) sharing are present . The extensive family structure within GS:SFHS also meant the duoHMM method could be applied to that cohort. The duoHMM method combined the results of a MCMC algorithm with pedigree information to improve phasing accuracy . HapMap phase II b37 was used to calcu […]


A population specific reference panel empowers genetic studies of Anabaptist populations

Sci Rep
PMCID: 5519631
PMID: 28729679
DOI: 10.1038/s41598-017-05445-3

[…] To build the AGRP, we first phased the genomes with SHAPEIT2. All known relationships were provided for phasing and the–duohmm option was enabled to make SHAPEIT2 incorporate pedigree information into the haplotype estimates, which has been shown to greatly improve the phasing accuracy. In order to keep as many as hapl […]


Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

PLoS Genet
PMCID: 5480811
PMID: 28640878
DOI: 10.1371/journal.pgen.1006328

[…] d alignment in Plink v1.9 [] to ensure all genotypes were reported on the forward strand, and kept only autosomal SNPs. To speed up imputation, data were first pre-phased with Shapeit v2 [] using the duoHMM option that combines pedigree information to improve phasing and default values for window size (2Mb), per-SNP conditioning sates (100), effective population size (n = 15000) and genetic maps f […]


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duoHMM institution(s)
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK ; Department of Statistics, University of Oxford, Oxford, UK ; Wellcome Trust Sanger Institute, Hinxton, UK ; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ; Institute for Maternal and Child Health - IRCCS Burlo Garofolo, University of Trieste, Trieste, Italy ; Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy ; Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy ; MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK ; Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK ; Faculty of Medicine, University of Split, Split, Croatia ; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI), Uganda Research Unit on AIDS, Entebbe, Uganda ; Laboratoire Génomique, Bioinformatique, et Applications (EA4627), Conservatoire National des Arts et Métiers, Paris, France
duoHMM funding source(s)
Supported by Wellcome Trust, grant number 090058/Z/09/Z and United Kingdom Medical Research Council, grant number G0801823.

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