Allele Frequency using different kits versions: Agilent SureSelect Human All Exon V4 and V5

Question

[m.bamajboor]

I have a question regarding the kits used for sequencing. I'm in a process of calculating the allele frequency of a group of samples, I have the VCF files however it was produced using different versions such as Agilent SureSelect Human All Exon V4 , V5 and V6. My question is, for calculating the AF, can I do my calculations with all files regardless of the version? or I should separate them?

Please note that I Calculate the allele frequency using VCFtools after Merging the filtered and normalized VCF files using BCFtools.

Thank you.