This can vary based on outcome-specific goals, however, typically the depth is to parallel or slightly below parallel. Some athletes who are looking to improve jump height may squat to 60-70 degrees of knee flexion to mimic jumping mechanics.
When looking to address sticking points, you can set your height just below the sticking point to be able to work through that difficult range. If your goal is maxima leg growth (muscular development), it may be best however to perform squats in the fullest range of motion, making box squats not as applicable in that scenario.