Let's say I have a vcf file (version 4.2). Then, I have a list of variants that I want to exclude from my VCF file. This list is a TXT file containing 3 columns: chromosome, position and ID (dbsnp) where available.
For example, lets say I have the data from this database:
Then I select the three columns of chromosome name, position and ID for dbsnp.
Is there anyway to remove these variants from my VCF files?