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Bioinformatics. 2015 Dec 15;31(24):4009-11. doi: 10.1093/bioinformatics/btv509. Epub 2015 Aug 30.

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

Author information

1
Center for GeoGenetics and.
2
Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.

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.

PMID:
26323718
PMCID:
PMC4673978
DOI:
10.1093/bioinformatics/btv509
[Indexed for MEDLINE]
Free PMC Article

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