Vieira, Filipe Garrett2; Fumagalli, Matteo2; Albrechtsen, Anders4; Nielsen, Rasmus5
1 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet2 University of California3 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet4 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet5 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet
impact on genotype calling and allele frequency estimation
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.