Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation.
Genome Res
; 23(11): 1852-61, 2013 Nov.
Article
em En
| MEDLINE
| ID: mdl-23950147
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.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Sequenciamento de Nucleotídeos em Larga Escala
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Frequência do Gene
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Genótipo
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Endogamia
Limite:
Animals
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Humans
Idioma:
En
Ano de publicação:
2013
Tipo de documento:
Article