GHap: an R package for genome-wide haplotyping

Yuri T. Utsunomiya; Marco Milanesi; Adam T. H. Utsunomiya; Paolo Ajmone Marsan; José F. Garcia

doi:10.1093/bioinformatics/btw356

GHap: an R package for genome-wide haplotyping

Yuri T. Utsunomiya
, Marco Milanesi
, Adam T. H. Utsunomiya
, Paolo Ajmone Marsan
, José F. Garcia

Universidade Estadual Paulista Júlio de Mesquita Filho
International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics

Risultato della ricerca: Contributo in rivista › Articolo

12 Citazioni (Scopus)

Abstract

The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers.

Lingua originale	Inglese
pagine (da-a)	2861-2862
Rivista	Bioinformatics
Volume	32
DOI	https://doi.org/10.1093/bioinformatics/btw356
Stato di pubblicazione	Pubblicato - 2016

Keywords

genome-wide

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10.1093/bioinformatics/btw356

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title = "GHap: an R package for genome-wide haplotyping",

abstract = "The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers.",

keywords = "genome-wide, genome-wide",

author = "Utsunomiya, \{Yuri T.\} and Marco Milanesi and Utsunomiya, \{Adam T. H.\} and \{Ajmone Marsan\}, Paolo and Garcia, \{Jos{\'e} F.\}",

year = "2016",

doi = "10.1093/bioinformatics/btw356",

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volume = "32",

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journal = "Bioinformatics",

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AU - Utsunomiya, Yuri T.

AU - Milanesi, Marco

AU - Utsunomiya, Adam T. H.

AU - Ajmone Marsan, Paolo

AU - Garcia, José F.

PY - 2016

Y1 - 2016

N2 - The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers.

AB - The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers.

KW - genome-wide

UR - http://hdl.handle.net/10807/91442

U2 - 10.1093/bioinformatics/btw356

DO - 10.1093/bioinformatics/btw356

M3 - Article

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VL - 32

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EP - 2862

JO - Bioinformatics

JF - Bioinformatics

ER -

GHap: an R package for genome-wide haplotyping

Abstract

Keywords

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