I downloaded the following vcf file from https://www.internationalgenome.org/.
I wanted to first try and calculate allele frequencies, and then from there calculate allele frequencies based on populations and so on. However, I ran into an issue where while I was using plink, I would utilize the --vcf command to try and calculate frequencies. The frequencies were calculated, but the SNP names were missing. I used the following command in Git Bash on Windows:
plink --vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz --freq --out chr22datanew
I then tried to convert the file to plink binary (bed, bim, fam) to try and use that for the basis of the allele frequencies. I used the following commands:
plink --vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.vcf --make-bed --out chr22data
plink --bfile chr22data --freq --out chr22freqs
Once again, the frequencies were calculated with no issue, but the SNP names were missing. I checked the .fam file that was created, and the SNPs were there, but not in the .bim file. This may be a simple, elementary level question, but does anyone know how to fix this? I am using plink 1.9 instead of vcftools because I'm using a computer that runs on Windows OS.