Using bcftools to merge files of different individuals, getting only shared sites
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4 months ago
Jautis ▴ 500

Hello, I have two vcf files that include non-overlapping sets of individuals. I would like to merge these into one vcf file, keeping only sites that appear in each of the files. There used to be a way to do this using GATK, but that is no longer supported in GATK4.

It seems like this could be done using isec (to get sites) and then merge, restricting the output to those sites, but is there any way to do it in a single step?

vcf genotypes bcftools • 129 views
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