polyRAD

Genotype calling with uncertainty from sequencing data in polyploids and diploids

Research output: Contribution to journalArticle

Abstract

Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Bayesian genotype calling can mitigate these issues, but previously has only been implemented in software that requires a reference genome or uses priors that may be inappropriate for the population. Here we present several novel Bayesian algorithms that estimate genotype posterior probabilities, all of which are implemented in a new R package, polyRAD. Appropriate priors can be specified for mapping populations, populations in Hardy-Weinberg equilibrium, or structured populations, and in each case can be informed by genotypes at linked markers. The polyRAD software imports read depth from several existing pipelines, and outputs continuous or discrete numerical genotypes suitable for analyses such as genome-wide association and genomic prediction.

Original languageEnglish (US)
Pages (from-to)663-673
Number of pages11
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number3
DOIs
StatePublished - Mar 1 2019

Fingerprint

Polyploidy
Diploidy
Uncertainty
Genotype
Population
Software
Genome
Homozygote
Heterozygote
DNA Sequence Analysis
Alleles

Keywords

  • Bayesian
  • Calling
  • DNA
  • Genotype
  • Imputation
  • Next-generation
  • Nucleotide
  • Polymorphism
  • Polyploidy
  • Sequencing
  • Single

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

polyRAD : Genotype calling with uncertainty from sequencing data in polyploids and diploids. / Clark, Lindsay V.; Lipka, Alexander Edward; Sacks, Erik J.

In: G3: Genes, Genomes, Genetics, Vol. 9, No. 3, 01.03.2019, p. 663-673.

Research output: Contribution to journalArticle

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