IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0030906.html
   My bibliography  Save this article

Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids

Author

Listed:
  • Oliver Serang
  • Marcelo Mollinari
  • Antonio Augusto Franco Garcia

Abstract

The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical Bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species.

Suggested Citation

  • Oliver Serang & Marcelo Mollinari & Antonio Augusto Franco Garcia, 2012. "Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-13, February.
  • Handle: RePEc:plo:pone00:0030906
    DOI: 10.1371/journal.pone.0030906
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030906
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0030906&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0030906?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. David Gerard, 2023. "Double reduction estimation and equilibrium tests in natural autopolyploid populations," Biometrics, The International Biometric Society, vol. 79(3), pages 2143-2156, September.
    2. Ivone de Bem Oliveira & Rhewter Nunes & Lucia Mattiello & Stela Barros-Ribeiro & Isabela Pavanelli Souza & Alexandre Siqueira Guedes Coelho & Rosane Garcia Collevatti, 2019. "Research and partnership in studies of sugarcane using molecular markers: a scientometric approach," Scientometrics, Springer;Akadémiai Kiadó, vol. 119(1), pages 335-355, April.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0030906. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.