PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

Roeland E. Voorrips*, Marco C.A.M. Bink, Johannes W. Kruisselbrink, Herma J.J. Koehorst-van Putten, Eric van de Weg

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

29 Citations (Scopus)

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.

Original languageEnglish
Article number119
JournalMolecular Breeding
Volume36
DOIs
Publication statusPublished - 2016

Keywords

  • Haploblock
  • Haplotyping
  • Pedigree
  • SNP

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