Full Squats = High Bar Position
If you are doing "full" squats (atg, ata, etc) then, preferably, you should be using a high bar position. At the very bottom of the hole, the hips move forward to achieve full flexion and if you are using a low bar placement, then the back must flex to keep the bar's center of gravity over your foot.
Long story short (IMHO):
*Low bar position = parallel or below parallel, hips move back
*High bar position = full squat, hips move vertically
Squatting and Lower Back Pain (Part I)
Squat Rx #21 ("Hips Back")