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= Usage=
= Usage=
Users should follow the following steps to compile Minimac3 (if they downloaded the source files) or should skip them (if they downloaded the binary executable).
## EXTRACT MINIMAC3 AND COMPILE
tar -xzvf Minimac3.v1.0.0.tar.gz
cd Minimac3/
make
A typical Minimac3 command line for imputation is as follows
../bin/Minimac3 --refHaps refPanel.vcf \
--haps targetStudy.vcf \
--prefix testRun
Here <code>refPanel.vcf</code> is the reference panel used in VCF format (e.g. 1000 Genomes), <code>targetStudy.vcf</code> is the phased GWAS data in VCF format and <code>testRun</code> is the prefix for the output files. Some commonly used reference panels are available for download in [[#Reference Panels for Download| Reference Panels]]. See wiki page on [[Minimac3 Usage| Detailed Usage]] and [[Minimac3 Imputation Cookbook|Imputation Cookbook]] for further details on using '''Minimac3''' for imputation analysis.
Users can always type the following for further support:
Users can always type the following for further support:
