I need to merge two VCF files which contain different variants, something I can do with either vcf-merge (VCFtools) or BCFtools merge. By default, both assume that information is missing in positions listed in one file, but not in the other, which is represented as a dot (.) in the merger of both. However, vcf-merge has an option (-R) to use REF allele (0/0) instead of the default missing genotype. Unfortunately, I have not been able to find the same in bcftools, which is a shame because bcftools is much faster than VCFtools. And I am handling some pretty big VCF files...
That being said, is there any fast and easy way to do the same using bcftools? I put emphasis on the speed because this is precisely the reason why I am interested in bcftools in the first place.
Thanks for your help, it's much appreciated.