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 onboard 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.