Improved whole-chromosome phasing for disease and population genetic studies

  title={Improved whole-chromosome phasing for disease and population genetic studies},
  author={O. Delaneau and Jean-François Zagury and Jonathan Marchini},
  journal={Nature Methods},
  • O. Delaneau, Jean-François Zagury, Jonathan Marchini
  • Published 2012
  • Medicine, Biology
  • Nature Methods
  • SHAPEIT2 uses multithreading so that multiple cores can be used to phase whole chromosomes, allowing users to make the best use of their computational resources. We tested SHAPEIT2 on several large-sample, whole-chromosome data sets from a range of SNP genotyping chips (Supplementary Note 1). SHAPEIT2 outperforms other methods (Fig. 1a–c) in terms of switch error rate (SER) and the mean distance between switch errors (Supplementary Figs. 1 and 2). As compared to SHAPEIT1, SHAPEIT2 reduced SER… CONTINUE READING

    Figures and Topics from this paper.

    Explore Further: Topics Discussed in This Paper

    A reference panel of 64,976 haplotypes for genotype imputation
    • 1,117
    • PDF
    A global reference for human genetic variation
    • 6,827
    • PDF
    Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
    • 236
    • PDF
    Next-generation genotype imputation service and methods
    • 904
    • PDF


    Publications referenced by this paper.
    A new statistical method for haplotype reconstruction from population data.
    • 7,041
    • PDF
    A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
    • 3,206
    • Highly Influential
    • PDF
    MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • 1,841
    • Highly Influential
    • PDF
    A linear complexity phasing method for thousands of genomes
    • 1,239
    Genotype Imputation with Thousands of Genomes
    • 820
    • PDF
    Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
    • 811
    • PDF