title: PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees.
abstract: In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called "haploblocks". Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.
authors.affiliation: Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
authors.forename: Roeland E
authors.initials: RE
authors.lastname: Voorrips
authors.affiliation: Biometris, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands ; Hendrix Genetics Research, P.O. Box 114, 5830 AC Boxmeer, The Netherlands.
authors.forename: Marco C A M
authors.initials: MC
authors.lastname: Bink
authors.affiliation: Biometris, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands.
authors.forename: Johannes W
authors.initials: JW
authors.lastname: Kruisselbrink
authors.affiliation: Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
authors.forename: Herma J J
authors.initials: HJ
authors.lastname: Koehorst-van Putten
authors.affiliation: Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
authors.forename: W Eric
authors.initials: WE
authors.lastname: van de Weg
keywords: Haploblock; Haplotyping; Pedigree; SNP