Joint calling

We don’t actually have to call variants on all your samples together to perform a joint analysis. We have developed a workflow that allows us to decouple the initial identification of potential variant sites (i.e. variant calling) from the genotyping step, which is the only part that really needs to be done jointly. This is the so-called "GVCF workflow", which utilizes a GVCF intermediate to allow scaling joint calling efficiently and conveniently.