In the best-case scenario, you have a VCF file with proper filters applied. If this is the case, you can just go ahead and use your file. Note that all VCF files will have a FILTER column, but this might not mean that all of the proper filters were applied. You have to be sure that your data is properly filtered.
In the second case, which is one of the most common, your file will have unfiltered data, but you'll have enough annotations and can apply hard filters (there is no need for programmatic filtering). If you have a GATK annotated file, refer to http://gatkforums.broadinstitute.org/discussion/2806/howto-apply-hard-filters-to-a-call-set.
In the third case, you have a VCF file that has all the annotations that you need, ...
