Promethease can read VCF, but there is a lot of flexibility in the VCF format.
Ideally you'll be able to produce a version 4.2 compliant VCF, with the END= fields set. This is sometimes known as a gVCF. That will be allow us to distinguish positions which match the reference from positions which were not callable due to insufficient sequencing depth. This will provide the best possible Promethease report.
Alternatively you could use GATK with --EMIT-ALL-SITES which produces a MUCH larger VCF file, that also allows us to know reference vs missing.
Lastly a standard VCF will work, but will not have any information about positions that match the reference. While not essential these can be helpful for a Promethease report.