Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Estimating inbreeding coefficients from NGS data : impact on genotype calling and allele frequency estimation. / Garrett Vieira, Filipe Jorge; Fumagalli, Matteo; Albrechtsen, Anders; Nielsen, Rasmus.

In: Genome Research, Vol. 23, 2013, p. 1852-1861.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Garrett Vieira, FJ, Fumagalli, M, Albrechtsen, A & Nielsen, R 2013, 'Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation', Genome Research, vol. 23, pp. 1852-1861. https://doi.org/10.1101/gr.157388.113

APA

Garrett Vieira, F. J., Fumagalli, M., Albrechtsen, A., & Nielsen, R. (2013). Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Research, 23, 1852-1861. https://doi.org/10.1101/gr.157388.113

Vancouver

Garrett Vieira FJ, Fumagalli M, Albrechtsen A, Nielsen R. Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Research. 2013;23:1852-1861. https://doi.org/10.1101/gr.157388.113

Author

Garrett Vieira, Filipe Jorge ; Fumagalli, Matteo ; Albrechtsen, Anders ; Nielsen, Rasmus. / Estimating inbreeding coefficients from NGS data : impact on genotype calling and allele frequency estimation. In: Genome Research. 2013 ; Vol. 23. pp. 1852-1861.

Bibtex

@article{59280bca1d7d42b1b31d25da91ef7f42,
title = "Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation",
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 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 beforecalling 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 datasets.",
author = "{Garrett Vieira}, {Filipe Jorge} and Matteo Fumagalli and Anders Albrechtsen and Rasmus Nielsen",
year = "2013",
doi = "10.1101/gr.157388.113",
language = "English",
volume = "23",
pages = "1852--1861",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",

}

RIS

TY - JOUR

T1 - Estimating inbreeding coefficients from NGS data

T2 - impact on genotype calling and allele frequency estimation

AU - Garrett Vieira, Filipe Jorge

AU - Fumagalli, Matteo

AU - Albrechtsen, Anders

AU - Nielsen, Rasmus

PY - 2013

Y1 - 2013

N2 - 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 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 beforecalling 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 datasets.

AB - 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 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 beforecalling 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 datasets.

U2 - 10.1101/gr.157388.113

DO - 10.1101/gr.157388.113

M3 - Journal article

C2 - 23950147

VL - 23

SP - 1852

EP - 1861

JO - Genome Research

JF - Genome Research

SN - 1088-9051

ER -

ID: 50812281