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

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

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 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).

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
Conference Name
Journal ISSN
Volume Title
Oxford University Press (OUP)
All rights reserved
European Research Council (647787)