Non variants sites of the genome (gVCF file)

Question

[heureuse]

Hello,

I have 10000 individuals and I would like to create a file where I put all the non variants sites and their coverage. The problem is that theses non variants sites are note the same from one individual to another. How to harmonize in order to avoid getting a huge file ? Maybe I can create a region with all the positions which are near and have the same coverage ? I really don't know how to overcame this.

Thank you in advance for your help.

[LauferVA]

Hi Heureuse ... do you have to use a gVCF? Or could you use another format?