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

被引：73

作者：

Vieira, Filipe G. ^{[1
]}

Fumagalli, Matteo ^{[1
]}

Albrechtsen, Anders ^{[2
]}

Nielsen, Rasmus ^{[1
,2
]}

机构：

[1] Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA

[2] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

来源：

GENOME RESEARCH | 2013年 / 23卷 / 11期

关键词：

WILD-RICE; LINKAGE DISEQUILIBRIUM; NUCLEOTIDE VARIATION; MULTILOCUS ANALYSIS; ORYZA-RUFIPOGON; POPULATION; GENOME; DOMESTICATION; ASSOCIATION; DISCOVERY;

D O I：

10.1101/gr.157388.113

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1852 / 1861

页数：10

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