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.
Utsunomiya, Y. T., Milanesi, M., Utsunomiya, A. T. H., Ajmone Marsan, P., Garcia, J. F., GHap: an R package for genome-wide haplotyping, <<BIOINFORMATICS>>, 2016; 32 (18): 2861-2862. [doi:10.1093/bioinformatics/btw356] [http://hdl.handle.net/10807/91442]
GHap: an R package for genome-wide haplotyping
Milanesi, MarcoSecondo
;Ajmone Marsan, PaoloPenultimo
;
2016
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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