Changes

<font face=Courier>"--haps"</font> denotes the main input GWAS file which has to be a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory.  

<font face=Courier>"--haps"</font> denotes the main input GWAS file which has to be a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory.  

Minimac3 can handle only VCF files as input for the target/gwas data. Note that input VCF files would be automatically assumed to be pre-phased. Markers which are in the target panel and NOT in the reference panel would be excluded from the output files. User must merge these extra markers back to the original data in order to analyze them.

Minimac3 can handle only VCF files as input for the GWAS data (see page on [[Minimac3 Cookbook : Converting Files to VCF|Converting Files to VCF]]). Note that input VCF files would be automatically assumed to be pre-phased (see page on [[Minimac3 Cookbook : Pre-Phasing|Pre-Phasing]]). Markers which are in the target panel and NOT in the reference panel would be excluded from the output files. User must merge these extra markers back to the original data in order to analyze them.

==Output Files==

==Output Files==