I have two vcf files from different project. One has 200 animals, the latter has 4000 animals. Before merging them into one file, I just realized the both vcf files have some missing genotypes. It is shown as ./.
Bcftools merge has an option to set the missing genotypes as 0/0. I am not completely sure if I should use this option or not. In next step I will add annotation and split the merged file to the seperate vcf files for each populations. Last I will look at the allele frequency of populations. Does 0/0 affect the AF calculation?
Thanks for the suggestions in advance!