Changes

After the pre-phasing has been done, we can begin to run the imputation. But before that,we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files) and also download the reference panels required for imputation. Consequently, we would have the following steps.

After the pre-phasing has been done, we can begin to run the imputation. But before that,we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files) and also download the reference panels required for imputation. Consequently, we would have the following steps.

===Converting GWAS Panel Files into VCF ===

===Convert GWAS Panel Files into VCF ===

If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.

If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.