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

Year: 2019
Type: article
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).
Source: GigaScience
DOI: 10.1093/gigascience/giz034
Institutions: University of Copenhagen, Centre National de la Recherche Scientifique, Université Toulouse III - Paul Sabatier, Natural History Museum of Denmark, Centre d'Anthropobiologie et de Génomique de Toulouse, Université de Toulouse, University of Cambridge
Language: English
Subfield: Genetics
Open Access status: gold
Estimated APC paid: $2,638
Funders: National Research Foundation, Danmarks Grundforskningsfond, Carlsbergfondet, Lundbeckfonden, Danmarks Frie Forskningsfond, H. Lundbeck A/S, H2020 European Research Council
OpenAlex ID: W2943389067
FWCI: 7.025
Cites: 29
Cited by: 215
Related to: 10