I'm kind of new to this space-- a friend of mine says he uses SNPeff for all his exome annotations, and he doesn't know of any other popular tools for this purpose.

 I'm annotating some human exomes and I am curious about what else is out there. A search gave me a lot of answers, but I don't know which are popular in the community. Are there gaps the SNPeff leaves that other effect predictors fill? Thank you so much for reading my post!
The tools I hear used most frequently are SnpEff, VEP, and Annovar. This [paper][1] (Table 1) shows a comparison of the three tools. 

SnpEff tends to be robust and I personally use it the most. Remarkably, SnpEff can effectively annotate even structural variants and long indels, in addition to traditional smaller variants. I've used Annovar once or twice but strange bugs crop up here and there; however the developer of it maintains it well and offers a lot of [documentation][2]. VEP seems quite popular, but I personally have the least experience with this one.


  [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4
  [2]: http://annovar.openbioinformatics.org/en/latest/