Delaneau, Olivier; Zagury, Jean-François; Robinson, Matthew RichardIST Austria ; Marchini, Jonathan L.; Dermitzakis, Emmanouil T.
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.
Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nature Communications. 2019;10:5436. doi:10.1038/s41467-019-13225-y
Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature Communications, 10, 5436. https://doi.org/10.1038/s41467-019-13225-y
Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications 10 (2019): 5436. https://doi.org/10.1038/s41467-019-13225-y.
O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” Nature Communications, vol. 10, p. 5436, 2019.
Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436.
Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications, vol. 10, Springer Nature, 2019, p. 5436, doi:10.1038/s41467-019-13225-y.