In dcgerard/updogAlpha: Using Parental Data for Offspring Genotyping

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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) [@elshire2011robust] or restriction site-associated DNA sequencing (RAD-Seq) [@baird2008rapid]. For such NGS data there exist other methods for genotyping --- see for example ebg [@blischak2017snp] and TET [@maruki2017genotype]. 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 @serang2012efficient and @li2011statistical 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 @shirasawa2017high 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: ``` {r, eval = FALSE}

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](https://doi.org/10.1101/281550).

Or, using BibTex:
``` tex
@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

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