What Muscles Do Squats Target?
In my view, squats are not as total-body as deadlifts. Anyway, best to do both because synergy. Barbell squats are of course the best stressor for building or maintaining lower body strength, but there are plenty of squat exercises in the Calisthenic category that are worth doing in a Calisthenics routine:
Goblet squats
Regular body-weight squats
Squat jumps
Box jumps
Squats plus, eg squats + overhead press, squats + curls, squat+heavy ball throws, etc.
Why Calisthenics category? Because they are lower stress, mainly aerobic endurance things that can be done daily without more than 24 hr recovery.