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Improved whole-chromosome phasing for disease and population genetic studies

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Figure 1: Accuracy and computational performance.


  1. Howie, B. et al. Nat. Genet. 44, 955–959 (2012).

    CAS  Article  Google Scholar 

  2. Delaneau, O., Marchini, J. & Zagury, J.F. Nat. Methods 9, 179–181 (2012).

    CAS  Article  Google Scholar 

  3. Howie, B.N., Marchini, J. & Stephens, M. G3 1, 457–470 (2011).

    Article  Google Scholar 

  4. Williams, A.L. et al. Am. J. Hum. Genet. 91, 238–251 (2012).

    CAS  Article  Google Scholar 

  5. Browning, S.R. & Browning, B.L. Am. J. Hum. Genet. 81, 1084–1097 (2007).

    CAS  Article  Google Scholar 

  6. Li, Y. et al. Genet. Epidemiol. 34, 816–834 (2010).

    Article  Google Scholar 

  7. Scheet, P. & Stephens, M. Am. J. Hum. Genet. 78, 629–644 (2006).

    CAS  Article  Google Scholar 

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J.M. and O.D. acknowledge support from the Medical Research Council (G0801823). O.D. acknowledges support from Peptinov SAS (France). Thanks to B. Howie, C. Churchhouse and J. O'Connell for comments on this paper and to A. Cox (Illumina Cambridge Ltd) for providing the high-coverage trio sequence data set. The Vietnamese cohort was provided by A. Alcais (Institut National de la Santé de la Recherche Médicale, Paris, France) and E. Schurr (McGill Centre for the Study of Host Resistance, Montreal, Canada). This study uses data from the Wellcome Trust Case Control Consortium.

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Correspondence to Jean-Francois Zagury or Jonathan Marchini.

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Supplementary Table 1, Supplementary Figures 1–7, Supplementary Methods and Supplementary Notes 1 and 2 (PDF 7498 kb)

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SHAPEIT2 software (ZIP 1281 kb)

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Delaneau, O., Zagury, JF. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 10, 5–6 (2013).

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