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Here <font face=Courier>refPanel.m3vcf</font> is the reference panel used in M3VCF format (e.g. 1000 Genomes), <font face=Courier>targetStudy.vcf</font> is the phased GWAS data in VCF format, and <font face=Courier>testRun</font> is the prefix for the output files.
Here <font face=Courier>refPanel.m3vcf</font> is the reference panel used in M3VCF format (e.g. 1000 Genomes), <font face=Courier>targetStudy.vcf</font> is the phased GWAS data in VCF format, and <font face=Courier>testRun</font> is the prefix for the output files.
If the reference panel is in VCF format, please use Minimac3 to convert it into M3VCF format first.
=== Convert VCF to M3VCF ===
If the reference panel is in VCF format, please use [[Minimac3]] to convert it into M3VCF format first.
../bin/Minimac3 --refHaps refPanel.vcf \
../bin/Minimac3 --refHaps refPanel.vcf \
--processReference \
--processReference \
