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

Gigascience 2019 05;8(5)

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark.

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).

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http://dx.doi.org/10.1093/gigascience/giz034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488770PMC
May 2019
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NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data
Korneliussen et al.
Bioinformatics 2015

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