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In the present study, two important effects of soil that is, soil amplification and foundation-soil flexibility are investigated on the seismic vulnerability of a four storey RC frame building, using a decoupled analysis approach. Four well-defined sites belonging to the same site class (ASCE 7-10 site class D) and varying bedrock depth are chosen to demonstrate the effect of local site conditions on seismic performance and vulnerability of the structure located on these sites. ASCE 41 methodology is used to model the structure- foundation system and to obtain the capacity curves using nonlinear static analysis procedure. The HAZUS methodology is then used to estimate the vulnerability curves for these buildings. The results on the four sites belonging to the same site class, show that the seismic performance and vulnerability of the RC frame building for a given amplitude of ground motion varies significantly with soil stratification and depth of bedrock.