Idan, > Is there an option to create a GTiff with a sparse index? [...] > Is there an option to eliminate this huge index
No, the index must be fully present in a TIFF file. > or an alternative format > that I can translate the vrt into and will be with a reasonable size? The GeoPackage driver will not emit sparse tiles, but currently only with RGBA Byte data (when alpha=0 for a tile), or single-band Float32 (when data for a tile matches the nodata value) Even -- Spatialys - Geospatial professional services http://www.spatialys.com
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