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