README.md

In dcgerard/updogAlpha: Using Parental Data for Offspring Genotyping

updogAlpha: Using Parental Data for Offspring Genotyping

This is the original code for the updog procedure. To use the new updog package, please see here.

This package will fit an empirical Bayesian procedure to genotype autopolyploid individuals from reduced-representation next-generation sequencing (NGS) data, such as genotyping by sequencing (GBS) (Elshire 2011) or restriction site-associated DNA sequencing (RAD-Seq) (Baird 2008). For such NGS data there exist other methods for genotyping --- see for example ebg (Blischak, Kubatko, and Wolfe 2017) and TET (Maruki and Lynch 2017). updog adds to this field by:

• Incorporating hierarchical structure into the genotyping procedure by either assuming the population consists of siblings (either an F1 or S1 population), or the population is in Hardy-Weinberg equilibrium. Though see Serang (2012) and Li (2011) for other discussion on this.
• Estimating sequencing error for each SNP.
• Accounting for read-mapping bias.
• Incorporating overdispersion, a key indicator for the quality of a SNP.
• Automatically accounting for outlying observations.
• Beautifully plotting the NGS data (see plot.updog).
• Running a simple goodness of fit test (see summary.updog).
• Simulating under a fitted model (see rupdog).

We've included a few SNP's from the data of Shirasawa et al. (2017) to show off the features of updog. See snpdata.

A vignette is available here.

Please report any bugs/issues here.

Installation

To install, run the following code in R:

# install.packages("devtools")
devtools::install_github("dcgerard/updog")

Citation

If you find the methods in this package useful, please cite

Gerard, D., Ferrão L.F.V., Garcia, A.A.F., & Stephens, M. (2018). Harnessing Empirical Bayes and Mendelian Segregation for Genotyping Autopolyploids from Messy Sequencing Data. bioRxiv. doi: 10.1101/281550.

Or, using BibTex:

@article {gerard2018harnessing,
    author = {Gerard, David and Ferr{\~a}o, Luis Felipe Ventorim and Garcia, Antonio Augusto Franco and Stephens, Matthew},
    title = {Harnessing Empirical Bayes and Mendelian Segregation for Genotyping Autopolyploids from Messy Sequencing Data},
    year = {2018},
    doi = {10.1101/281550},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2018/03/16/281550},
    eprint = {https://www.biorxiv.org/content/early/2018/03/16/281550.full.pdf},
    journal = {bioRxiv}
}

References

Baird, Paul D. AND Atwood, Nathan A. AND Etter. 2008. “Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers.” PLOS ONE 3 (10). Public Library of Science: 1–7. doi:10.1371/journal.pone.0003376.

Blischak, Paul, Laura Kubatko, and Andrea Wolfe. 2017. “SNP Genotyping and Parameter Estimation in Polyploids Using Low-Coverage Sequencing Data.” bioRxiv. Cold Spring Harbor Labs Journals. doi:10.1101/120261.

Elshire, Jeffrey C. AND Sun, Robert J. AND Glaubitz. 2011. “A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species.” PLOS ONE 6 (5). Public Library of Science: 1–10. doi:10.1371/journal.pone.0019379.

Li, Heng. 2011. “A Statistical Framework for SNP Calling, Mutation Discovery, Association Mapping and Population Genetical Parameter Estimation from Sequencing Data.” Bioinformatics 27 (21): 2987. doi:10.1093/bioinformatics/btr509.

Maruki, Takahiro, and Michael Lynch. 2017. “Genotype Calling from Population-Genomic Sequencing Data.” G3: Genes, Genomes, Genetics 7 (5). G3: Genes, Genomes, Genetics: 1393–1404. doi:10.1534/g3.117.039008.

Serang, Marcelo AND Garcia, Oliver AND Mollinari. 2012. “Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids.” PLOS ONE 7 (2). Public Library of Science: 1–13. doi:10.1371/journal.pone.0030906.

Shirasawa, Kenta, Masaru Tanaka, Yasuhiro Takahata, Daifu Ma, Qinghe Cao, Qingchang Liu, Hong Zhai, et al. 2017. “A High-Density SNP Genetic Map Consisting of a Complete Set of Homologous Groups in Autohexaploid Sweetpotato (Ipomoea Batatas).” Scientific Reports 7. Nature Publishing Group. doi:10.1038/srep44207.

dcgerard/updogAlpha documentation built on May 14, 2019, 3:10 a.m.