Let's keep it simple:
If the words after "yes" and "no" echo/repeat the words of the question, use a comma.
...Did you clock in that morning as usual?
...Yes, I did.
...No, I did not.
...Were you with your brother?
...Yes, I was with my brother.
...No, I wasn't.
Use a period for everything else.
...Did you clock in that morning as usual?
...No. I was ten minutes late.
...Yes. I was never late.
...Were you with your brother?
...No. He stayed home.
...Yes. My sister joined us also.
NOTE: The words but and because don't change this.
...Did you leave at 5:00?
...Yes. But I seemed to be the only one.
...No. Because I had an appointment, I left at 4:30.
This makes this a simple issue where agonizing over punctuation does not really buy you extra readability.
Happy punctuating -- and wishing you a safe and celebratory Fourth of July!
Margie