Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding
Open accessAbstract
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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No first- or second-degree relatives were found among the Ancient Rapanui, and a single pair of third- to fourth-degree relatives was detected.
“Using READ42 and NGSrelate243, we did not find any first- or second-degree relatives among the Ancient Rapanui (Supplementary Figs. 23 and 24 and Supplementary Information section 9) and detected a single pair of third- to fourth-degree relatives on the basis of IBD sharing (highest estimated IBD sharing >15 cM between any two individuals is <1,000 cM; Supplementary Information section 8 and”
From Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas (2024) · cites this paper as [43]
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Self-citationAncient Rapanui genomes reveal resilience and pre-European contact with the Americas
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“Using READ 42 and NGSrelate2 43 , we did not find any first-or second-degree relatives among the Ancient Rapanui (Supplementary Figs.”
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Self-citation
- Authors
- Hanghøj, K., Moltke, I., Andersen, P. A., Manica, A., & Korneliussen, T. S.
- Affiliations
- University of Copenhagen (DK)
- University of Cambridge (GB)
- Corresponding author
- Hanghøj, Kristian
- Korneliussen, Thorfinn Sand
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-04-30
- Volume
- 8
- Issue
- 5
- Pages
- giz034
- ISSN
- 2047-217X (ISSN-L)
- PMC
- PMC6488770
- OpenAlex
- W2943389067
- Cited by
- 216
- References
- 28
- Citations by year
- 2026: 43 · 2025: 48 · 2024: 40 · 2023: 33 · 2022: 21 · 2021: 22 · 2020: 7 · 2019: 2
- FWCI
- 7.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- GigaScience (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- HAL (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Danish National Research Foundation (DNRF94)
- Initiative d'Excellence Chaires d'attractivité, Université de Toulouse
- Carlsberg Foundation (CF16-0913)
- Danish National Research Foundation Centre for GeoGenetics (DNRF 0094)
- Lundbeck Foundation GeoGenetics Centre for Brain, Disease, & Evolution (R302-2018-2155)
- Independent Research Fund Denmark (DFF - 4090-00244)
- ERC Consolidator (647787)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- relatedness estimation, inbreeding, low-pass sequencing, genotype calls, high-throughput sequencing data
- MeSH terms
- Genetics, Population, Genotype, Humans, Inbreeding, Software, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, High-Throughput Nucleotide Sequencing, Genotyping Techniques
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