The Linac Coherent Light Source (LCLS) is a fourthgeneration light source demonstration project based on the self-amplified spontaneous emission (SASE) free-electron laser (FEL) concept. It will combine a new photoinjector, the Stanford Linear Accelerator Center (SLAC) linac, with two stages of bunch compression and a long undulator to create intense radiation pulses at 1.5 A. Successful operation of the LCLS will require consistent delivery of a highbrightness electron beam to the undulator, in the face of effects such as wakefields and coherent synchrotron radiation (CSR). Because of the sensitivity to beam quality and subtle effects, it is necessary to perform integrated tracking from the cathode through the undulator. We report on the combined use of PARMELA, elegant, and GENESIS to perform these simulations, and in particular the simulation of pulse-to-pulse variation in FEL performance due to rfand laser-related variation in the electron beam.