I'm using HaplotypeCaller on a family that is unusual; it has two affected children and one unaffected parent. The disease is expected to be caused by a homozygous or compound heterozygous mutation, and the unaffected parent is a carrier. We don't have any sequence data on the other unaffected parent. So obviously the variants I am interested in are going to be common among all three samples, i.e., child1, child2 and parent. I ran HaplotypeCaller on each sample seperately. I now have 3 vcf files. How can I filter the common variants among them? I have added read groups that show the relationship with tags 'c1' 'c2' and 'p' (for child1, child2 and parent). Or should I go back and rerun HaplotypeCaller but this time input all three sample files together and specify one output vcf? I am reluctant to do this as it took about 8 days for each of my HaplotypeCaller runs to finish the last time. [plus I actually have 6 families to do this on, not one].
Please help. And appreciate your support