Reference Panel download

[Shrishtee-kandoi]

Hi Minimac4 Team,

I am currently facing challenges while attempting to run "minimac4" to impute my genotype files on our High-Performance Cluster. I have encountered a couple of issues that I believe may require your expertise to resolve.

Reference Panel Download: I attempted to download the reference panel from the provided link on the Minimac4 wiki page .. However, despite connecting to the FTP server, the download does not initiate. I would appreciate guidance on the correct procedure or any potential troubleshooting steps.

Target Study VCF File: I want to confirm if the "targetStudy.vcf" file mentioned in the documentation refers to the VCF file generated from Plink files using the following commands from :

plink --bfile YOURFILE --keep-allele-order --freq --out YOURFILE.output --allow-no-sex
plink --bfile YOURFILE --recode vcf --out YOURFILE.output_file --keep-allele-order
vcf-sort YOURFILE.output_file.vcf | bgzip -c > pre_impute_YOURFILE.vcf.gz

Is this the correct process for creating the target VCF file for Minimac4 imputation?

Imputation Code: For imputation, I am using the following code:

minimac4 --refHaps refPanel.m3vcf \
         --haps targetStudy.vcf \
         --prefix testRun \
         --cpus 5

Is "refPanel.m3vcf" downloadable from the link above? and Can I substitute "targetStudy.vcf" with "pre_impute_YOURFILE.vcf.gz" in this command?

Your assistance in resolving these issues would be immensely valuable, and I appreciate your time and support in advance.

Thank you!