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Record number 507052
Title PediHaplotyper : software for consistent assignment of marker haplotypes in pedigrees
Author(s) Voorrips, Roeland E.; Bink, Marco C.A.M.; Kruisselbrink, Johannes W.; Koehorst-van Putten, Herma J.J.; Weg, Eric van de
Source Molecular Breeding 36 (2016). - ISSN 1380-3743
DOI http://dx.doi.org/10.1007/s11032-016-0539-y
Department(s) WUR PB Kwantitatieve Aspecten
PE&RC
Biometris (PPO/PRI)
Sports Centre Algemeen
WUR PB Siergewassen, Tissue Culture
WUR PB Biodiversiteit en Genetische Variatie
EPS
Publication type Refereed Article in a scientific journal
Publication year 2016
Keyword(s) Haploblock - Haplotyping - Pedigree - SNP
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.

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