Shedding of droplets in a flow focusing junction is standard technique in two-phase microfluidics. This break-up is driven by a capillary instability. Here we present a depth-averaged approach to simulate these complex phenomena. Since the physical mechanism of the instability is three-dimensional we add modified boundary conditions that account for necking. We predict the control parameters, center flow and cross flow rate at given capillary number and viscosity ratio, in order to obtain desired shedding frequency and droplet volume.