PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data

Roeland E. Voorrips*, Giorgio Tumino

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Background: For genetic analyses, multi-allelic markers have an advantage over bi-allelic markers like SNPs (single nucleotide polymorphisms) in that they carry more information about the genetic constitution of individuals. This is especially the case in polyploids, where individuals carry more than two alleles at each locus. Haploblocks are multi-allelic markers that can be derived by phasing sets of closely-linked SNP markers. Phased haploblocks, similarly to other multi-allelic markers, will therefore be advantageous in genetic tasks like linkage mapping, QTL mapping and genome-wide association studies. Results: We present a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays, which is applicable to polyploids. This method is implemented in the software package PolyHaplotyper. In contrast to existing packages for polyploids it makes use of full-sib families among the samples to guide the haplotyping process. We show that in this situation it is much more accurate than other available software, using experimental hexaploid data and simulated tetraploid data. Conclusions: Our method and the software package PolyHaplotyper in which it is implemented extend the available tools for haplotyping in polyploids. They perform especially well in situations where one or more full-sib families are present.

Original languageEnglish
Article number442
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 23 Oct 2022


  • Haplotype
  • Multi-allelic marker
  • Polyploid
  • SNP array


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