What is a good pipeline for using public domain exomes as controls?
I gather that you want to use the background SNP frequency as a prior for input to your SNP calling algorithm?

I'm not sure of a canned algorithm for doing this, but a quick google shows up some promising links:


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722/
https://software.broadinstitute.org/gatk/documentation/article.php?id=4723
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0489-0