Is there a good way to distinguish ./. from 0/0 in a merged vcf? For example, a tool that goes back to the bam files for missing genotypes and checks if it's homozygous reference or a NO CALL? I would imagine this would be important to do, especially in 30x WGS where there are a lot of low coverage areas that lead to no calls.
Although, I guess if you have the bam files maybe the best thing to do is joint variant calling?