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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

NgsRelate : a software tool for estimating pairwise relatedness from next-generation sequencing data. / Korneliussen, Thorfinn Sand; Moltke, Ida.

In: Bioinformatics (Oxford, England), Vol. 31, No. 24, 2015, p. 4009-4011.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Korneliussen, TS & Moltke, I 2015, 'NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data', Bioinformatics (Oxford, England), vol. 31, no. 24, pp. 4009-4011. https://doi.org/10.1093/bioinformatics/btv509

APA

Korneliussen, T. S., & Moltke, I. (2015). NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. Bioinformatics (Oxford, England), 31(24), 4009-4011. https://doi.org/10.1093/bioinformatics/btv509

Vancouver

Korneliussen TS, Moltke I. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. Bioinformatics (Oxford, England). 2015;31(24):4009-4011. https://doi.org/10.1093/bioinformatics/btv509

Author

Korneliussen, Thorfinn Sand ; Moltke, Ida. / NgsRelate : a software tool for estimating pairwise relatedness from next-generation sequencing data. In: Bioinformatics (Oxford, England). 2015 ; Vol. 31, No. 24. pp. 4009-4011.

Bibtex

@article{2912866b164342ff8a53ccb5d0ee2c8d,
title = "NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data",
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.pop gen.dk/software.CONTACT: ida@binf.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.",
author = "Korneliussen, {Thorfinn Sand} and Ida Moltke",
note = "{\textcopyright} The Author 2015. Published by Oxford University Press.",
year = "2015",
doi = "10.1093/bioinformatics/btv509",
language = "English",
volume = "31",
pages = "4009--4011",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "24",

}

RIS

TY - JOUR

T1 - NgsRelate

T2 - a software tool for estimating pairwise relatedness from next-generation sequencing data

AU - Korneliussen, Thorfinn Sand

AU - Moltke, Ida

N1 - © The Author 2015. Published by Oxford University Press.

PY - 2015

Y1 - 2015

N2 - 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.pop gen.dk/software.CONTACT: ida@binf.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.

AB - 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.pop gen.dk/software.CONTACT: ida@binf.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.

U2 - 10.1093/bioinformatics/btv509

DO - 10.1093/bioinformatics/btv509

M3 - Journal article

C2 - 26323718

VL - 31

SP - 4009

EP - 4011

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 24

ER -

ID: 145240626