Haplotype, legend, sample, and genetic map files
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Download packages (warning: large files)
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This download contains reference data for 1,011 individuals from Africa, Asia, Europe, and the Americas. We provide one worldwide haplotype file for each chromosome since we recommend using all available reference haplotypes with IMPUTE2, regardless of the ancestry of your study data. For background information on this approach, see here.
If you really want to use just a subset of the haplotypes, you can manually parse the haplotype files with a utility like the linux 'cut' command. The sample file that comes in the download package contains the information needed to subset the files.
When using these combined panels, you should set the -Ne argument of IMPUTE2 to 20000, as explained here.
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