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Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.

Accepted version
Peer-reviewed

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Authors

Hanghøj, Kristian 
Moltke, Ida 
Andersen, Philip Alstrup 
Korneliussen, Thorfinn Sand 

Abstract

BACKGROUND: The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data. RESULTS: We introduce ngsRelateV2, a major revision of ngsRelateV1, a program that originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process. CONCLUSION: The program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).

Description

Keywords

Jacquard coefficients, genotype likelihood, high-throughput sequencing data, inbreeding, next-generation sequencing, population genetics, relatedness estimation, threading, Genetics, Population, Genotype, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Humans, Inbreeding, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Software

Journal Title

Gigascience

Conference Name

Journal ISSN

2047-217X
2047-217X

Volume Title

8

Publisher

Oxford University Press (OUP)

Rights

All rights reserved
Sponsorship
European Research Council (647787)