In a high-bar squat, the barbell sits on the traps and basically as high up as you can get it without it sitting on your actual neck.
This keeps the load a little closer to the center line, resulting in a more upright torso position. This causes greater ankle mobility demands, and greater bias of tension in the quads.
In a low-bar squat, the barbell sits lower, on the "shelf" that your posterior delts create. This creates a more forward lean, utilizing the posterior chain. While less ankle mobility is required, there will be a greater demand for shoulder and thoracic mobility.
Your ideal set up will depend heavily on your leverages, mobility and strengths.
For example; Becky has long femurs, a short torso, crap ankle dorsiflexion, and excellent shoulder mobility. Therefore a low-bar squat is an excellent option. The slight lean forwards, utilizes the greater thoracic and shoulder mobility, while also biasing tension in the glutes
and back. Which in Becky's case, are much stronger!