The navigation stack supports obstacle avoidance from 3D point clouds out of the box. Here's the tutorial:
http://wiki.ros.org/navigation/Tutorials/RobotSetup#Costmap_Configuration_.28local_costmap.29_.26_.28global_costmap.29
It's better to ask this kind of question over at
https://answers.ros.org/. If you encounter problems while following the tutorial, create a question over there and copy a link here, I'll try to answer.
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