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=== Impute Samples ===
=== Impute Samples ===
The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download|below]] or created on a previous run of Minimac3).
../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \
--haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
--prefix Gwas.Chr20.Imputed.Output
../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.m3vcf \
--haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
--prefix Gwas.Chr20.Imputed.Output
= Chromosome X Imputation =
= Chromosome X Imputation =
