Question: I can't squat deep at all. What should I do?
Answer: You probably need to stretch your hammies.
I've had countless arguments with people about this. The simplistic notions that people harbor really amaze me. But yes, many people think that if you stretch your hammies for awhile you will be handed an "ass to grass" squat by the stretching fairy. Not even close to being anywhere remotely in the ballpark of reality. There is so much that goes into developing the mobility and stability needed to have a deep and heavy back squat.
Check out this post by Bill Hartman: Stability Training Reduces Hamstring Stiffness
To start it is a great example of what you can and cannot infer from a 'study'. But Bill brings also brings up some great examples of how flexibility training isn't always as obvious as it seems. The interplay between stability and mobility can be tricky to understand intuitively.
Also, see Mike Robertson's article The Mobility/Stability Continuum
On Eric Cressey's site check out: