GHap: an R package for genome-wide haplotyping | Zendy

Yuri Tani Utsunomiya | Zendy; Marco Milanesi | Zendy; Adam Taiti Harth Utsunomiya | Zendy; Paolo AjmoneMarsan | Zendy; José Fernando Garcia | Zendy

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GHap: an R package for genome-wide haplotyping

Author(s) -

Yuri Tani Utsunomiya,

Marco Milanesi,

Adam Taiti Harth Utsunomiya,

Paolo AjmoneMarsan,

José Fernando Garcia

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw356

Subject(s) - haplotype , r package , allele , computer science , 1000 genomes project , sample (material) , genotype , haplotype estimation , computational biology , genetics , biology , programming language , single nucleotide polymorphism , gene , physics , thermodynamics

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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