To automate the procedure of reducing large amounts of variants into a small subset of functionally important variants, a script (auto_annovar.pl) is provided in the ANNOVAR package. By default, auto_annovar.pl performs a multi-step procedure by executing ANNOVAR multiple times, each time with several different command line parameters, and generates a final output file containing the most likely causal variants and their corresponding candidate genes. For recessive diseases, this list can be further trimmed down to include genes with multiple variants that are predicted to be functionally important.
