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

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 maj...

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Detalles Bibliográficos
Autores principales: Hanghøj, Kristian, Moltke, Ida, Andersen, Philip Alstrup, Manica, Andrea, Korneliussen, Thorfinn Sand
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488770/
https://www.ncbi.nlm.nih.gov/pubmed/31042285
http://dx.doi.org/10.1093/gigascience/giz034
Descripción
Sumario: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).