Work

NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

Year: 2015

Type: article

Abstract: MOTIVATION: Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty. RESULTS: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. AVAILABILITY: NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btv509

Authors: Thorfinn Sand Korneliussen, Ida Moltke

Institution: University of Copenhagen

Language: English

Topic: Genetic diversity and population structure

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,989

Funders: National Research Foundation, Danmarks Grundforskningsfond, Danmarks Frie Forskningsfond