Changes

=== Imputation into Phased Haplotypes - minimac(2)===

=== Imputation into Phased Haplotypes - minimac(2)===

Imputing genotypes using '''minimac(2)''' 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 ''aliases'' file that provides mappings between earlier marker names and the current preferred name for each polymorphism.

Imputing genotypes using '''minimac(2)''' 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.  

 

Minimac needs a file listing the variants in your sample. If your directory already includes a "sample.snps" file, no worries. If it doesn't, you can generate one using "sample.dat" as input with the following command:

 

  cut -f 2 -d " " sample.dat > sample.snps

The minimac command line would look like this:

The minimac command line would look like this: