The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
Accurate, scalable and integrative haplotype estimation
Open accessAbstract
The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.
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Cites
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationThe variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,200
The UK Biobank resource with deep phenotyping and genomic data
Bycroft, C., Freeman, C., Petkova, D., Band, G., Elliott, L. T., Sharp, K., Motyer, A., Vukcevic, D., Delaneau, O., O’Connell, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0579-z · Cited by 8,876
Self-citationLi, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,486
Howie, B. N., Donnelly, P., & Marchini, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000529 · Cited by 3,928
Self-citationNext-generation genotype imputation service and methods
Das, S., Forer, L., Schönherr, S., Sidore, C., Locke, A. E., Kwong, A., Vrieze, S. I., Chew, E. Y., Levy, S., McGue, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3656 · Cited by 3,808
Browning, S. R., & Browning, B. L. (2007) · The American Journal of Human Genetics · doi:10.1086/521987 · Cited by 3,210
A reference panel of 64,976 haplotypes for genotype imputation
the Haplotype Reference Consortium (2016) · Nature Genetics · doi:10.1038/ng.3643 · Cited by 2,836
A One-Penny Imputed Genome from Next-Generation Reference Panels
Browning, B. L., Zhou, Y., & Browning, S. R. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.07.015 · Cited by 2,092
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Cited by
Byrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094
Fast two-stage phasing of large-scale sequence data
Browning, B. L., Tian, X., Zhou, Y., & Browning, S. R. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.08.005 · Cited by 888
Accurate detection of identity-by-descent segments in human ancient DNA
Ringbauer, H., Huang, Y., Akbari, A., Mallick, S., Olalde, I., Patterson, N., & Reich, D. (2024) · Nature Genetics · doi:10.1038/s41588-023-01582-w · Cited by 155
Community-wide genome sequencing reveals 30 years of Darwin’s finch evolution
Enbody, E. D., Sendell-Price, A. T., Sprehn, C. G., Rubin, C.-J., Visscher, P. M., Grant, B. R., Grant, P. R., & Andersson, L. (2023) · Science · doi:10.1126/science.adf6218 · Cited by 75
50,000 years of evolutionary history of India: Impact on health and disease variation
Kerdoncuff, E., Skov, L., Patterson, N., Banerjee, J., Khobragade, P., Chakrabarti, S. S., Chakrawarty, A., Chatterjee, P., Dhar, M., Gupta, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.027 · Cited by 36
Metadata
- Authors
- Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T.
- Venue
- Nature Communications
- Published
- 2019-11-28
- Volume
- 10
- Issue
- 1
- Pages
- 5436-5436
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2990059271
- Cited by
- 622
- References
- 31
- FWCI
- 24.11
- Type
- journal article
- Language
- en
- Open access
- gold
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- Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature Communications. https://doi.org/10.1038/s41467-019-13225-y
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