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

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12 Citations (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.

Original language	English
Pages (from-to)	2861-2862
Journal	Bioinformatics
Volume	32
DOIs	https://doi.org/10.1093/bioinformatics/btw356
Publication status	Published - 2016

Keywords

genome-wide

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10.1093/bioinformatics/btw356

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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.",

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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

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VL - 32

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JO - Bioinformatics

JF - Bioinformatics

ER -

GHap: an R package for genome-wide haplotyping

Abstract

Keywords

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