I have exome sequences from 6 families (~38 samples) of European descent with similar hereditary diseases (e.g. epilepsy). Each family is supposedly unrelated. Some samples are from healthy family members, others are infected. What's the best way to do joint genotyping for this type of analysis? Should I (i) do joint genotyping on all 38 samples, then split them into individual vcf afterwards (for variant analysis), or (ii) do joint genotyping only for samples in the same family (so 6 separate joint-genotypings)? Also, let's say my samples comprise of different ethnicities, is it still better to do joint-genotyping or it won't really improve the variant calling in this case? Thanks for your help!