We present an end-to-end modeling framework, spanning the device, module and also system levels, for analyzing thin film photovoltaics (PV). This approach is based on embedding a detailed, statistically relevant, physics based equivalent circuit into module and array level simulations. This approach enables us to analyze key variability and reliability issues in thin film PV, and allows us to interpret their effect on process yield and intrinsic module lifetimes. Our results suggest that the time-zero gap between cell and module efficiencies, a key variability concern for thin-film PV, can be attributed to processrelated shunts with log-normal PDF distributed randomly across the cell surface. Similarly, this end-to-end simulation approach allows us to investigate the reliability issues caused by partial shadowing in thin film modules, especially in context of array configurations. These results provide important insights into its nature and consequences of shadow degradation on long term system performance. This work showcases the importance of an integrated analysis in case of thin film PV, because traditional approaches used to Silicon PV to tackle reliability/variability issues cannot be applied directly to such systems.