Calculate allelic richness from vcf/plink data.

Question

[K]

I am a student working on a population genetics project, focusing on counting allelic richness. My dataset is originally in VCF format, which I have converted to PLINK files. I have downloaded the R package hierfstat to calculate allelic richness and count the number of alleles in my samples. However, I am facing challenges using the PLINK files directly with this package. Despite searching through available resources and literature, I have not found clear guidance on the steps to extract or format the data for this purpose. I would greatly appreciate advice or detailed instructions on how to process PLINK or VCF files to calculate allelic richness using hierfstat.