I'm having a problem obtaining a recoded vcf which contains variants with their IDs in a "snp file" OR their positions in a "position file." The following gives only variants with their IDs in the "snp file" AND their positions in the "position file."
vcftools --vcf <input vcf file> --snps <variant IDs file> --positions <variant positions file> --recode --out <output vcf file>
Is there any way that I can obtain that which I desire without having to do each separately, concatenating, and then getting rid of duplicates?
Thanks in advance.