I am trying to remove entries in the VCF file based on rs_id. I tried to use bcftools view but for some reason preparing a list of the positions I need to be excluded did not work.
A sample of the file looked like this:
22 rs165886 22 rs165608 22 rs1541529 22 rs4819925 22 rs5992604
and the bcftools command is the following:
bcftools view -T ^tlist.txt input.vcf
which always give an error
Could not parse the file
so I tried to change the value in the plink map file to -1 like the below, and then I recoded it again using plink to vcf. even after all of that, the positions are still in the vcf file.
22 rs165886 -1 17339003 22 rs165608 -1 17339404
Can you please tell me how to fix this?