vcftools- extract allele frequencies from pooled samples on a sample by sample basis

Question

[straderm]

I am looking to extract minor allele frequencies using vcftools for pooled samples on a sample by sample basis, as allele frequency output by vcftools is only on a site basis. Further, the reference alleles should be polarized (same ref allele).

[4galaxy77]

Use bcftools +fill-tags, as vcftools is deprecated and should no longer be used.