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GHap: an R package for genome-wide haplotyping.
Utsunomiya, Yuri T; Milanesi, Marco; Utsunomiya, Adam T H; Ajmone-Marsan, Paolo; Garcia, José F.
Affiliation
  • Utsunomiya YT; Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, São Paulo, Brazil International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-68
  • Milanesi M; International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 Araçatuba, São Paulo, Brazil Departamento de Apoio, Produção e Saúde Animal, UNESP - Univ. Estadual Paulista, Faculdade de Medicina Veterinária de Araçatuba, 16050-680 Araçatuba, São Paulo
  • Utsunomiya AT; International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 Araçatuba, São Paulo, Brazil Departamento de Apoio, Produção e Saúde Animal, UNESP - Univ. Estadual Paulista, Faculdade de Medicina Veterinária de Araçatuba, 16050-680 Araçatuba, São Paulo
  • Ajmone-Marsan P; Istituto di Zootecnica, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy.
  • Garcia JF; Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, São Paulo, Brazil International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-68
Bioinformatics ; 32(18): 2861-2, 2016 09 15.
Article in En | MEDLINE | ID: mdl-27283951
ABSTRACT
UNLABELLED 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. AVAILABILITY AND IMPLEMENTATION https//cran.r-project.org/package=GHap CONTACT ytutsunomiya@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Haplotypes / Software Type of study: Prognostic_studies Limits: Humans Language: En Journal: Bioinformatics Year: 2016 Document type: Article
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PubMed Links
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Haplotypes / Software Type of study: Prognostic_studies Limits: Humans Language: En Journal: Bioinformatics Year: 2016 Document type: Article