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Accurate, scalable and integrative haplotype estimation

Author

Listed:
  • Olivier Delaneau

    (University of Lausanne, Génopode
    University of Lausanne, Quartier Sorge – Batiment Amphipole)

  • Jean-François Zagury

    (HESAM Université)

  • Matthew R. Robinson

    (University of Lausanne, Génopode
    University of Lausanne, Quartier Sorge – Batiment Amphipole)

  • Jonathan L. Marchini

    (University of Oxford)

  • Emmanouil T. Dermitzakis

    (University of Geneva Medical School
    University of Geneva
    University of Geneva Medical School)

Abstract

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.

Suggested Citation

  • Olivier Delaneau & Jean-François Zagury & Matthew R. Robinson & Jonathan L. Marchini & Emmanouil T. Dermitzakis, 2019. "Accurate, scalable and integrative haplotype estimation," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13225-y
    DOI: 10.1038/s41467-019-13225-y
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    1. Lijing Tang & Benjamin Swedlund & Sébastien Dupont & Chad Harland & Gabriel Costa Monteiro Moreira & Keith Durkin & Maria Artesi & Eric Mullaart & Arnaud Sartelet & Latifa Karim & Wouter Coppieters & , 2024. "GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Robin J. Hofmeister & Simone Rubinacci & Diogo M. Ribeiro & Alfonso Buil & Zoltán Kutalik & Olivier Delaneau, 2022. "Parent-of-Origin inference for biobanks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Xinkai Tong & Dong Chen & Jianchao Hu & Shiyao Lin & Ziqi Ling & Huashui Ai & Zhiyan Zhang & Lusheng Huang, 2023. "Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Parker C. Wilson & Yoshiharu Muto & Haojia Wu & Anil Karihaloo & Sushrut S. Waikar & Benjamin D. Humphreys, 2022. "Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    6. Seppe Goovaerts & Hanne Hoskens & Ryan J. Eller & Noah Herrick & Anthony M. Musolf & Cristina M. Justice & Meng Yuan & Sahin Naqvi & Myoung Keun Lee & Dirk Vandermeulen & Heather L. Szabo-Rogers & Pau, 2023. "Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    7. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    8. Junhui Yuan & Sanjie Jiang & Jianbo Jian & Mingyu Liu & Zhen Yue & Jiabao Xu & Juan Li & Chunyan Xu & Lihong Lin & Yi Jing & Xiaoxiao Zhang & Haixin Chen & Linjuan Zhang & Tao Fu & Shuiyan Yu & Zhangy, 2022. "Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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