Currently PhenoTips is unable to process zipped vcf files, however users are not prompted with an error when selecting them (e.g. user can select and *.vcf.gz file in the dialog, however once dialog is closed the file isn't present on the patient record form).
It would be useful to add this ability as some of our users are likely to be having them.
Users should be prompted if they chose any vcf.* file format that PhenoTips does not support.