Joint Calling

why do we need to do joint calling?

if we are still comparing to a reference, the joint calling is going to use the actual read data from many samples together to give you moe statistial power and calling variance.

The reference is just a static string. it never changes, it's just the I mean for a given reference build. it just says that at the site there's an A. and then for each of your individual samples you actually have a read data. that's going to tell you it's pretty common that there's a G here in the population. so that's going to inform the variant calls we make at that site.