How can I identify common variants in siblings with same disorder after joint calling?

Question

[pragnapcu]

With the help of GATK GenomicsDBImport and Genotypegvcf, I have jointly called variants in siblings and done hardfiltering. I am puzzled about how to find out common variants in these two samples. Could someone please help me out?

[Pierre Lindenbaum]

eg. : Finding shared genotypes between multiple VCF files