I have a primary office but often talk with clients via phone and video and do paperwork at home does that qualify as a home office

If the area of your home where these calls, etc., take place is not specifically designated as an "office" that is used exclusively for your business, then it does not qualify as a home office.

Can I specify home office if I have a desk and file cabinet in the room where the communications and paperwork take place

Do you only use the desk and file cabinet for this work?  If you do, then the area it takes up can be considered an office (even if it is only a small percentage of your home).  The program will ask the total size of your home and the area you use exclusively for business.  (Don't expect a big refund on this, but every penny counts.)