You don’t need to do this to prepare your data for a candidate gene study. You only need it when you want to download the source hapmap.org text data files.
Downloading hapmap data
You can download the hapmap.org data with a program “ge-fetch-hapmap”. It’s a script written in Python. It runs on GNU/Linux and Microsoft Windows.
$ ./ge-fetch-hapmap --help
Usage: ge-fetch-hapmap [options]
Options:
-h, --help show this help message and exit
-c FILE, --config=FILE
Configuration file
-p PROXY, --proxy=PROXY
HTTP Proxy
This program uses a configuration file, hapmap.ini.
; Configuration for hapmap.org data download.
;
; Author: Maciej Blizinski <maciej.blizinski@gmail.com>
[hapmap]
; The base URL
Base URL: http://www.hapmap.org/downloads/phasing/2006-07_phaseII/phased/
; Chromosomes to download, for example: 1-22, X
; Chromosomes: 1-3, 5, X
Chromosomes: 1-22, X
; Populations, in form of FILE_NAME(ANALYSIS_NAME), where FILE_NAME
; denotes part of the hapmap filename to download and ANALYSIS_NAME
; denotes the name used in analysis.
Populations: CEU (Eur), JPT+CHB (Asian), YRI (Afr)
; Directory for hapmap data
Data directory: hapmap-data
; Directory for original hapmap files
Download directory: download
After the script has finished, the download directory will contain compressed and uncompressed data files. If you download all chromosomes, the directory will occupy about 800MB of disk space.
Last modified on Tue Feb 26 07:53:16 +0000 2008