IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v100y2015icp79-87.html
   My bibliography  Save this article

A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids

Author

Listed:
  • Ferretti, Luca
  • Ramos-Onsins, Sebástian E.

Abstract

Several variations of the Watterson estimator of variability for Next Generation Sequencing (NGS) data have been proposed in the literature. We present a unified framework for generalized Watterson estimators based on Maximum Composite Likelihood, which encompasses most of the existing estimators. We propose this class of unbiased estimators as generalized Watterson estimators for a large class of NGS data, including pools and trios. We also discuss the relation with the estimators proposed in the literature and show that they admit two equivalent but seemingly different forms, deriving a set of combinatorial identities as a byproduct. Finally, we give a detailed treatment of Watterson estimators for single or multiple autopolyploid individuals.

Suggested Citation

  • Ferretti, Luca & Ramos-Onsins, Sebástian E., 2015. "A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids," Theoretical Population Biology, Elsevier, vol. 100(C), pages 79-87.
  • Handle: RePEc:eee:thpobi:v:100:y:2015:i:c:p:79-87
    DOI: 10.1016/j.tpb.2015.01.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580915000027
    Download Restriction: Full text for ScienceDirect subscribers only

    File URL: https://libkey.io/10.1016/j.tpb.2015.01.001?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Rachel Brenchley & Manuel Spannagl & Matthias Pfeifer & Gary L. A. Barker & Rosalinda D’Amore & Alexandra M. Allen & Neil McKenzie & Melissa Kramer & Arnaud Kerhornou & Dan Bolser & Suzanne Kay & Darr, 2012. "Analysis of the bread wheat genome using whole-genome shotgun sequencing," Nature, Nature, vol. 491(7426), pages 705-710, November.
    2. RoyChoudhury, Arindam & Wakeley, John, 2010. "Sufficiency of the number of segregating sites in the limit under finite-sites mutation," Theoretical Population Biology, Elsevier, vol. 78(2), pages 118-122.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Vogl, Claus & Bergman, Juraj, 2015. "Inference of directional selection and mutation parameters assuming equilibrium," Theoretical Population Biology, Elsevier, vol. 106(C), pages 71-82.
    2. Vogl, Claus & Clemente, Florian, 2012. "The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates," Theoretical Population Biology, Elsevier, vol. 81(3), pages 197-209.
    3. Burden, Conrad J. & Tang, Yurong, 2017. "Rate matrix estimation from site frequency data," Theoretical Population Biology, Elsevier, vol. 113(C), pages 23-33.
    4. Osama Tahir & Sajid Ali Khan Bangash & Muhammad Ibrahim & Sana Shahab & Sahir Hameed Khattak & Israr Ud Din & Muhammad Nauman Khan & Aqsa Hafeez & Sana Wahab & Baber Ali & Rania M. Makki & Steve Harak, 2022. "Evaluation of Agronomic Performance and Genetic Diversity Analysis Using Simple Sequence Repeats Markers in Selected Wheat Lines," Sustainability, MDPI, vol. 15(1), pages 1-20, December.
    5. Vogl, Claus, 2014. "Estimating the scaled mutation rate and mutation bias with site frequency data," Theoretical Population Biology, Elsevier, vol. 98(C), pages 19-27.
    6. Vogl, Claus & Mikula, Lynette C. & Burden, Conrad J., 2020. "Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation–drift model," Theoretical Population Biology, Elsevier, vol. 134(C), pages 106-118.

    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:eee:thpobi:v:100:y:2015:i:c:p:79-87. 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.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with 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: Catherine Liu (email available below). General contact details of provider: https://www.journals.elsevier.com/intelligence .

    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.