I have a list of ~1,400 sites that I would like to remove from any VCF generated from a particular genotyping chip. (These are sites that our lab's indepedent QC procedure for that chip has flagged as problematic for one reason or another.)
I had hoped that there would be a way to specify those sites in a file that I could pass as an argument to some
bcftools command, but I can't find this functionality in the documentation.
(The closest I have found is the functionality that, as far as I can tell from the rather opaque documentation, does exactly the opposite of what I want. Here I'm referring to the
--regions-file option of the
bcftools view command. As far I as I can tell, this option instructs
bcftools view to produce a VCF file consisting only of the sites (or regions) specified in the file that one passes as this option's argument.)
I'd prefer to do this site removal with
bcftools (since I am already using
bcftools for other processing steps), but I'll use something else if
bcftools really does not have a good way to do what I am trying to do.
Thanks in advance for any advice!