Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation (original) (raw)

1. Matteo Fumagalli1,
2. Anders Albrechtsen2 and
3. Rasmus Nielsen1,2
4. 1Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA;
5. 2Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark

Abstract

Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.

Footnotes

• ↵3 Corresponding author
  E-mail fgarrettvieira{at}gmail.com

• [Supplemental material is available for this article.]

• Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.157388.113.

• Received March 7, 2013.

• Accepted August 6, 2013.

• © 2013 Vieira et al.; Published by Cold Spring Harbor Laboratory Press

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