I work for this company, so I am biased. iVariantGuide is an easy to use web-based tool that takes VCFs as input (4.1 or higher) and will annotate the file and provide graphical filtering and visualizations. It also can produce pathway enrichment analysis, GO analysis, and can produce an automated written summary. Currently the application has an unlimited trial, but some features are locked unless you get a subscription. It supports, single sample, paired sample, trios, and case-control multi-sample VCFs. Give it a try.

Here's a brief video describing the application.