I have exome datasets from 6 samples, in which four are affected and two are non-affected. I did joint call genotyping for all the six samples and annotated the vcf file. From this annotated vcf file, I have to look for rare variants shared by the four affected members.
First, I plan to filter all the rare variants which have allele frequency less than 1% (using Gnomad exome database in nonfinnish European population)
I don't how to proceed with next step, where look for rare variants shared by four affected individuals. So, should I check whether all the four individuals carry the alternate allele for a given variant?. Since, there is only one vcf file, how do I compare and see if the four affected individuals carry the alternate allele for a given variant?