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

Bioinformatics
Thorfinn Sand Korneliussen, Ida Moltke

Abstract

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. 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. NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software. ida@binf.ku.dk Supplementary data are available at Bioinformatics online.

References

Oct 1, 1975·Annals of Human Genetics·E A Thompson
Apr 1, 2009·Genetic Epidemiology·Yoonha ChoiBruce S Weir
Sep 3, 2010·Nature·UNKNOWN International HapMap 3 ConsortiumJean E McEwen
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Nov 26, 2014·BMC Bioinformatics·Thorfinn KorneliussenRasmus Nielsen
Jan 13, 2015·Trends in Genetics : TIG·Jason A O'RaweGholson J Lyon

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Citations

Feb 24, 2018·Science·Charleen GaunitzLudovic Orlando
Mar 5, 2020·Proceedings. Biological Sciences·Elisa G DierickxSimon H Martin
Apr 24, 2018·PloS One·Jose Manuel Monroy KuhnTorsten Günther
Jun 17, 2020·G3 : Genes - Genomes - Genetics·Emily HumbleJoseph I Hoffman
Apr 30, 2017·Science·Pablo LibradoLudovic Orlando

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Methods Mentioned

BETA
chip

Software Mentioned

PLINK
ANGSD
NgsRelate

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