Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage.

ABSTRACT: The site frequency spectrum is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the site frequency spectrum from called genotypes introduces bias when working with low-coverage sequencing data. Methods exist for addressing this issue but sometimes suffer from 2 problems. First, they can have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multidimensional site frequency spectrum estimation. In this article, we present a stochastic expectation-maximization algorithm for inferring the site frequency spectrum from NGS data that address these challenges. We show that this algorit

SUBMITTER: Rasmussen MS 

PROVIDER: S-EPMC9713400 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature