Thrombosis commonly develops in the left atrial appendage of patients with atrial fibrillation. The formation of blood clots in atrial appendage is a complex process, which depends on the shape of the appendage, the velocity of blood flow, the concentrations of red blood cells, platelets, and coagulation, among other factors. In this work, we present a new methodology to identify the key factors contributing to clot formation in the left atrial appendage during atrial fibrillation. The new methodology combines computed tomography imaging, computational fluid dynamics, mesh processing, and multiphase thrombosis modeling. We begin by running simulations to investigate flow patterns inside the left atrial appendages with realistic geometries. Our simulations suggest that at the entrance of the left atrial appendage the flow forms vortices, which can intrude inside the appendage depending on the phases of the cardiac cycle. Next, we introduce blood coagulation and consider different scenarios corresponding to physiological values of blood flow velocity, geometry of the left atrial appendage, and hematocrit values. Numerical results suggest that the chances of clot formation are higher in the "cactus" geometry than in the "chicken-wing" one, in agreement with the literature. Furthermore, they suggest that slower flow circulation facilitates the development of a clot in the depth of the left atrial appendage. Slower blood movement also favors the procoagulant activity of platelets, while faster flow circulation enhances the procoagulant effect from erythrocytes. Finally, our simulations show that increased hematocrit upregulates the generation of fibrin polymer, regardless of flow velocity.