Hi everybody,

I am wondering what is the best approach to deal with sites that are not present in all VCF when combining multiple vcf files. For example, a site may be homozygous for reference in several VCFs. One way is to leave them untyped, as if there are not sufficient coverage. Another way is to assume them as homozygous for reference. A third way may be to look into the alignment files (when they are available). In the last case, how can I be sure that a site is homozygous reference without doing a variant calling?

Thanks!