This tool is not deprecated, but this article is now superseded by the method article on JEXL expressions.
VariantFiltration
For a complete, detailed argument reference, refer to the GATK document page here.
The documentation for Using JEXL expressions within the GATK contains very important information about limitations of the filtering that can be done; in particular please note the section on working with complex expressions.
Filtering Individual Genotypes
One can now filter individual samples/genotypes in a VCF based on information from the FORMAT field: Variant Filtration will add the sample-level FT tag to the FORMAT field of filtered samples (this does not affect the record's FILTER tag). This is still a work in progress and isn't quite as flexible and powerful yet as we'd like it to be. For now, one can filter based on most fields as normal (e.g. GQ < 5.0), but the GT (genotype) field is an exception. We have put in convenience methods so that one can now filter out hets (isHet == 1), refs (isHomRef == 1), or homs (isHomVar == 1).