It’s a common belief that squatting to parallel is bad for the knees. Because of this it is not uncommon to see people half-squatting or quarter-squatting with a barbell or on a Smith machine. Unfortunately this is a myth. Squatting above parallel is actually one of the worst things you can do for your knees.
When you focus on squats above parallel, you keep the pressure on your anterior chain. Anterior chain muscles include quads and abs. This creates an uneven sheer force which causes the patella tendon to pull forward and grind on the femur. Needless to say, this is very bad for the knees.
By squatting to parallel you bring into play the posterior chain muscles, including the hamstrings, hips and glutes. This helps to balance this shear force, making the squat a much safer exercise.