NgsRelate
Computational Tool
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General Information
DescriptionA software tool for estimating pairwise relatedness from next-generation sequencing data
Homepagehttp://www.popgen.dk/software
Publications
NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data
Thorfinn Sand Korneliussen; Ida Moltke
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.
Contact : ida@binf.ku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
DOI: https://doi.org/10.1093/bioinformatics/btv509
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