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Imputing genotypes using '''minimac''' is an easy and 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 the model parameter estimation, imputation should proceed rapidly.
Imputing genotypes using '''minimac''' is an easy and 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 the model parameter estimation, imputation should proceed rapidly.
=== Creating SNP List File ===
'''Minimac''' requires a file listing markers in the haplotype file. This file can be easily generated by extracting the first column from the .info file created during the MaCH haplotyping process. In a standard Unix system, a command like this should do:
cut -f 1 target.info > target.snps
=== Running Minimac ===
=== Running Minimac ===
