It's a bit of an apples vs oranges comparison. Annovar is for Annotating Variants, that is, it annotates existing variant calls. Syzygy (I am assuming you mean this one: http://www.broadinstitute.org/software/syzygy/) performs variant (SNP and indel) calling on pooled samples, which is one conceptual step before you would use Annovar. It is possible that Syzygy also does some annotation but I see it mainly as a pooled variant caller.