I have a large VCF (WGS >7000 samples) that I converted to plink bfile with this command

plink --vcf in.vcf --make-bed --out plink

A fam file is produced, but does not reflect the relationships, phenotypes, or genders

I've replaced the fam file with a correct one containing these information. Then I calculate allele frequency with this command

plink --bfile plink --freq counts --out plink

I've noticed that the allele counts are incorrect, like for variant A plink reports an allele count of 1 and when I manually parse the VCF, I find the allele count is 3 (for founders only)

So something went wrong.

How do I convert a VCF into a plink bfile while replacing/updating the fam file, so I don't get these errors.