Scripts for testing the error rate of polyRAD

Dataset

Description

This set of scripts accompanies the manuscript describing the R package polyRAD, which uses DNA sequence read depth to estimate allele dosage in diploids and polyploids. Using several high-confidence SNP datasets from various species, allelic read depth from a typical RAD-seq dataset was simulated, then genotypes were estimated with polyRAD and other software and compared to the true genotypes, yielding error estimates.
Date made availableNov 21 2018
PublisherUniversity of Illinois at Urbana-Champaign

Keywords

  • R programming language
  • simulation
  • polyploidy
  • Bayesian genotype calling
  • restriction site-associated DNA sequencing (RAD-seq)
  • genotyping-by-sequencing (GBS)
  • single nucleotide polymorphism (SNP)

Research Output

polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids

Clark, L. V., Lipka, A. E. & Sacks, E. J., Mar 1 2019, In : G3: Genes, Genomes, Genetics. 9, 3, p. 663-673 11 p.

Research output: Contribution to journalArticle

Open Access
  • Cite this

    Clark, L. V. (Creator), Lipka, A. E. (Creator), Sacks, E. J. (Creator) (Nov 21 2018). Scripts for testing the error rate of polyRAD. University of Illinois at Urbana-Champaign. 10.13012/B2IDB-9729830_V2