Give a few more details on the knee problem. What tendon are you talking about? There's many in the knee. The parallel position of the squat is the point at which the greatest amount of pressure is on the patella (knee cap). If it's a patella tracking problem, parallel squats will def cause a problem. If not now, it'll start as soon as the cartilage begins to wear away on femur and/or underside of patella.
Shallow squats (approx. 30 +/- degress of flexion) are good if you can do them pain free. Despite the bad wrap they get from some, leg extensions are a great quad builder. It's probably going too heavy that causes the problems for some people. Go moderate weight, and flex at top for quite a while (3-10 seconds, or longer). You can get a great leg workout without squats or leg presses. It may take a while longer though, as you'll have to do more movements in the form of isolation work that will hit the muscles that squats/leg presses also worked i.e.) adductors/abductors, glutes, TFL, etc. You can get a good leg workout w/o putting excessive stress on the knee. I also like good mornings, stiff leg deads, partial sumo smith squats. Knees farther out also put less stress on the knee. Good advice from others regarding avoiding whatever movements cause the wrong kind of pain.
Where is the pain/inflammation? What other activities bother your knee?...walking/running/stairs? Do you stretch your lower body regularly? Any grinding sound/feel in the knee joint?
Not an expert. I used to love squatting deep, but can't do it now. A knee issues caused me to educate myself about the knee joint, and make (still trying various things) adjustements that work for me.