When the word so means “therefore,” it begins a new sentence and needs to be preceded by a semicolon or a period. It NEVER takes a single separating comma after it but can always have something after it that requires a pair of commas.
…We live near the beach; so there are issues with dampness and mold.
…The vegetation had grown up around the house; so we had to hire someone to clear it.
…So in the afternoon we left for the appointment.
…So we decided to accompany her.
…So, Your Honor, we will submit that in the morning.
…So, first, let me tell you my reasoning.