The authors' description of the software is that
"ANNOVAR is is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes."
whilst I am not a good enough programmer to comment on how efficient the code is, in the context of a 'why reinvent the wheel' ANNOVAR is definitely an efficient way to get started on doing exome / whole genome resequencing for variant discovery.
basically it is a collection of perl scripts that can do
1)take in variant information from popular tools like samtools-pileup , Complete Genomics, GFF3-SOLID (?), etc.
2) Do Annotation that is
The other nice thing is that the download already comes with excellent examples that you would be able to get going fast.
there's also annotation datasets avail for download from the developers
I only see hg18 for now though.
This page is a nice summary for beginners doing exome / whole genome resequencing.
UPDATE (2010Aug11): Users have reported a bug (double-counting of splicing) in the auto_annovar.pl program in the 2010Aug06 version. An updated version is provided here.