I am trying to convert my vcf file to a readable format in R using plink. Specifically, I want a .raw file to follow up the workflow of a recent paper.
I have tried:
plink --vcf myfile.vcf.gz --export A --out ofile --allow-extra-chr
but the SNP headers look like ".G" instead of "SNP1_1515.G". What is wrong here?
Edit: I know I can get the desired output using the .bim file, but was wondering about approximation in plink with one command.