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Minimac: 1000 Genomes Imputation Cookbook

3 bytes added, 11:24, 26 July 2013
Imputation into Phased Haplotypes - minimac
=== Imputation into Phased Haplotypes - minimac ===
Imputing genotypes using '''minimac''' is a straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for estimating model parameters (which describe the length and conservation of haplotype stretches shared between the reference panel and your study samples), imputation should proceed rapidly. Because marker names can change between dbSNP versions, it is usually a good idea to include an ''aliases'' file that provides mappings between earlier marker names and the current preferred name for each polymorphism.
A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:
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