multisample calling with GATK in diverse ethnic populations
I'm trying to generate a reference panel for imputation from WGS low coverage data from three different African populations using GATK. As data at all sites needs to be complete for a reference panel, the two ways of possibly doing this are multi-sample calling accross all three populations with GATK, or carrying out multi-sample calling per population, and then calling sites variant in any population separately per population prior to merging. I wasn't sure if multi-sample calling with GATK across genetically diverse populations may lead to issues, such as reduced calling of rare variants that appear in one population and not in others? Would you be able to clarify this, please?