I am working with some mouse exome capture data, and I would like to provide functional annotations to variants (SNPs and small indels).
For human data, I would typically use ANNOVAR. It looks like ANNOVAR allows users to create custom annotations (which could be applied to anything, including mouse data), but it generally seems to primarily specialize in human genome annotations (for example, wANNOVAR doesn't appear to work with anything except hg18 or hg19).
I've done a quick search and found some other options (SnpEff, Mouse SNP Miner, VEP in Ensembl, etc.), but I don't really know what is commonly used in the mouse genomics community. Any suggestions? If ANNOVAR is still the best option for mice, what are the most useful databases to download?