This came by on the live feed just before the end of the stage:

Questioned by letour.fr, Tinkoff-Saxo's directeur sportif Philippe Mauduit who jumped in the second team car to let a free seat to Alberto Contador after his retirement explained: “Alberto badly crashed. His right knee is seriously injured. The crash has been violent. I have his shoe with me, it's completely destroyed. According to some rumors, his bike has been broken but that's not the case. A bike fell from our racks after we fixed Nicolas Roche's bike. It's obviously too early to establish a diagnostic for Alberto. Once he'll reach the finish, he'll undergo an x-ray examination. Before pulling out, he told us that he was in an awful pain and he couldn't go any further on his bike. It's a pity because everything had gone well since the beginning of the Tour. We had a plan and today's race was unfolding exactly as we wanted. In a fraction of a second, it all fell apart, so we're immensely sad. Tomorrow, it's a rest day. After tomorrow, a new battle will begin. We'll stay united and a new Tour de France will begin for us.”