Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data.

ABSTRACT:

Background

The site frequency spectrum summarizes the distribution of allele frequencies throughout the genome, and it is widely used as a summary statistic to infer demographic parameters and to detect signals of natural selection. The use of high-throughput low-coverage DNA sequencing data can lead to biased estimates of the site frequency spectrum due to high levels of uncertainty in genotyping.

Results

Here we design and implement a method to efficiently and accurately estimate the multidimensional joint site frequency spectrum for large numbers of haploid or diploid individuals across an arbitrary number of populations, using low-coverage sequencing data. The method maximizes a likelihood function that represents the probability of the sequencing data observed given a m

SUBMITTER: Mas-Sandoval A 

PROVIDER: S-EPMC9112775 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature