The Galactic center (GC) is the densest region of the Milky Way. Variability surveys towards the GC potentially provide the largest number of variable stars per square degree within the Galaxy. However, high stellar density is also a drawback due to blending. Moreover, the GC is affected by extreme reddening, therefore near infrared observations are needed. We plan to detect new variable stars towards the GC, focusing on type II Cepheids (T2Cs) which have the advantage of being brighter than RR Lyrae stars. We perform parallel Lomb-Scargle and Generalized Lomb-Scargle periodogram analysis of the $K_s$-band time series of the VISTA variables in the Via Lactea survey, to detect periodicities. We employ statistical parameters to clean our sample. We take account of periods, light amplitudes, distances, and proper motions to provide a classification of the candidate variables. We detected 1,019 periodic variable stars, of which 164 are T2Cs, 210 are Miras and 3 are classical Cepheids. We also found the first anomalous Cepheid in this region. We compare their photometric properties with overlapping catalogs and discuss their properties on the color-magnitude and Bailey diagrams. We present the most extensive catalog of T2Cs in the GC region to date. Offsets in E($J-K_s$) and in the reddening law cause very large ($sim$1-2 kpc) uncertainties on distances in this region. We provide a catalog which will be the starting point for future spectroscopic surveys in the innermost regions of the Galaxy.
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