Cite as: Cold Spring Harb. Protoc.; 2008; doi:10.1101/pdb.prot5027

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Retrieving HapMap Data via Bulk Download

Albert Vernon Smith

This protocol was adapted from "Using the HapMap Web Site," Chapter 6, in Genetic Variation (eds. Weiner et al.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2007.


INTRODUCTION

The primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap Web site. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Bulk downloads of chromosome- or genome-wide data provide text dumps of the entire HapMap data set. Although complete, such downloads do not provide any filtering or selection services. This protocol describes the retrieval of HapMap data via bulk download.


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