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      Haploview: Visualization and analysis of SNP genotype data.

      Cold Spring Harbor protocols

      User-Computer Interface, Software, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Internet, Humans, Genotype, Databases, Genetic, Computer Graphics, methods, Computational Biology

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          Abstract

          Association studies involve accessing, parsing, generating, and analyzing large volumes of data, often carried out in many steps over many months. Large-scale surveys of genetic variation, such as the International HapMap Project, and rapidly increasing volumes of single-nucleotide polymorphism (SNP) genotyping data have created exciting opportunities for association studies. However, they have further exacerbated the difficulty of curating and analyzing such data. Haploview is a program developed in Mark Daly's lab at the Broad Institute of MIT and Harvard, which is designed to bundle many everyday analysis tasks into one easy-to-use package. Haploview has several features that are useful throughout different phases of association studies. Several of these features are illustrated in this article by following a hypothetical association study from design to execution. Haploview is used to (1) analyze HapMap data and choose tag-SNPs, (2) evaluate the quality of disease genotype data, (3) test for association, and (4) evaluate a region for follow-up of a positive association.

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          Journal
          10.1101/pdb.ip71
          20147036

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