We present a description of the design and usage of a new synoptic pipeline and data base model for time series photometry in the VISTA Data Flow System (VDFS). All UK Infra-Red Telescope Wide Field Camera (UKIRT) data and most of the VISTA main survey data will be processed and archived by the VDFS. Much of these data are multi-epoch, useful for finding moving and variable objects. Our new data base design allows the users to easily find rare objects of these types amongst the huge volume of data being produced by modern survey telescopes. Its effectiveness is demonstrated through examples using Data Release 5 of the UKIRT Deep Infrared Sky Survey (UKIDSS-Deep Extragalactic Survey (DXS) and the Wide Field Camera standard star data. The synoptic pipeline provides additional quality control and calibration to these data in the process of generating accurate light curves. We find that 0.6 +/- 0.1 per cent of stars and 2.3 +/- 0.6 per cent of galaxies in the UKIDSS-DXS with K <15 mag are variable with amplitudes ΔK > 0.015 mag.