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


BACKGROUND
NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software.
Center for GeoGenetics and.
Thorfinn Sand
TS
Korneliussen
Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
Ida
I
Moltke
D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016013:Likelihood Functions; D012984:Software