From Genome Analysis Wiki
→Group Rare Variants from Annotated VCF
* The annotated VCF file should be specified using --annotatedVcf option.
* --annotation should be used with --annotatedVcf together when specific category of functional variants are of interest to be grouped. For example, if grouping nonsynonymous and splicing variants are of interests, the following should be included in command line:
--annotatedVcf your.annotated.vcf --annotation nonsyn/splicing