Hi all.

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?

Many thanks.

Edit: I know I can get the desired output using the .bim file, but was wondering about approximation in plink with one command.