I have a list of positions (POS) in a text file I would like to remove from a .vcf file. What is the simplest way to do this? I have tried:
vcftools --vcf cluster_1_private.vcf --exclude remove_poly_1.txt --recode --recode-INFO-all --out cluster_1_fixed
but this doesnt seem to work, but note the text file only contains a list of numbers such as:
Maybe I need to specify the POS somehow?