Introduction

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.

Publications

  1. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data.
    Cite this
    Korneliussen TS, Moltke I, 2015-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Thorfinn Sand Korneliussen
    Developer

  2. Ida Moltke
    Investigator

    Department of Biology, University of Copenhagen, Denmark

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Summary
AccessionBT001497
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionDenmark
Submitted ByIda Moltke