How to drop specific sites from VCFs?
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11 days ago
kynnjo ▴ 50

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.

vcf • 158 views
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Entering edit mode
11 days ago
GenoMax 115k

Past thread with an answer that will be useful: Remove a list of positions form a VCF file