Illinois Data Bank - Dataset

Scripts for testing the error rate of polyRAD
Cite this dataset:
Clark, Lindsay V.; Lipka, Alexander E.; Sacks, Erik J. (2018): Scripts for testing the error rate of polyRAD. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9729830_V2
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.
Subject Life Sciences
Keywords R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
License CC BY
Funder U.S. National Science Foundation (NSF)-Grant:1661490
Corresponding Creator Lindsay V. Clark
Downloaded 818 times
Version DOI Comment Publication Date
2 10.13012/B2IDB-9729830_V2 All analyses were redone based on input from peer review of the corresponding manuscript. In particular, allelic read depth was simulated under a beta-binomial distribution rather than a binomial distribution, and comparisons to the software updog and fitPoly were added 2018-11-21
1 10.13012/B2IDB-9729830_V1 2018-08-01

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