If you are unable to squat to full depth then your joints aren’t doing what they are supposed to. The good news, there is a fix! Accumulating time in the bottom of a squat is not a new concept. Kelly Starrett of Mobility WODs has been advocating a 10 minute squat ‘test’ for several years now. Our friend Ido Portal also advocates squatting, asking his students to accumulate up to 30 minutes in a squat throughout the day, every day.
At first this may be difficult for you, but persevere. If you spend some time every day working on your squat the results won’t be far off.