Genotype-Frequency Estimation from High-Throughput Sequencing Data.

ABSTRACT: Rapidly improving high-throughput sequencing technologies provide unprecedented opportunities for carrying out population-genomic studies with various organisms. To take full advantage of these methods, it is essential to correctly estimate allele and genotype frequencies, and here we present a maximum-likelihood method that accomplishes these tasks. The proposed method fully accounts for uncertainties resulting from sequencing errors and biparental chromosome sampling and yields essentially unbiased estimates with minimal sampling variances with moderately high depths of coverage regardless of a mating system and structure of the population. Moreover, we have developed statistical tests for examining the significance of polymorphisms and their genotypic deviations from Hardy-Weinberg equi

SUBMITTER: Maruki T 

PROVIDER: S-EPMC4596663 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature