RT Journal
A1 Vieira, Filipe G.
A1 Fumagalli, Matteo
A1 Albrechtsen, Anders
A1 Nielsen, Rasmus
T1 Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
JF Genome Research 
JO Genome Research 
YR 2013 
FD November 01 
VO 23 
IS 11 
SP 1852 
OP 1861 
DO 10.1101/gr.157388.113 
UL http://genome.cshlp.org/content/23/11/1852.abstract 
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 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.