VCF : how to use

[gpcr]

Hi,
How to use hmmvar-func, if I have a list of many variants accross multiple genes in combined .VCF format from multiples exomes?
and also how are variant groups defined? is it based on genes/domain etc?
from examples :
87 P/Q 4
87 is AA position, P/Q is the change in AA. What is 4? how is it defined?

Thanks