Autonomous dual-arm manipulation is an essential skill to deploy robots in unstructured scenarios. However, this is a challenging undertaking, particularly in terms of perception and planning. Unstructured scenarios are full of objects with different shapes and appearances that have to be grasped in a very specific manner so they can be functionally used. In this paper we present an integrated approach to perform dual-arm pick tasks autonomously. Our method consists of semantic segmentation, object pose estimation, deformable model registration, grasp planning and arm trajectory optimization. The entire pipeline can be executed on-board and is suitable for on-line grasping scenarios. For this, our approach makes use of accumulated knowledge expressed as convolutional neural network models and low-dimensional latent shape spaces. For manipulating objects, we propose a stochastic trajectory optimization that includes a kinematic chain closure constraint. Evaluation in simulation and on the real robot corroborates the feasibility and applicability of the proposed methods on a task of picking up unknown watering cans and drills using both arms.