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This may have already been resolved but for future readers. Try QGIS' Saga Plugin > Grid Tools > Mosaick raster layers. You can combine a number of rasters and classify overlapping areas with blending, feathering, min and max values.


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Edit: Just read that this option was suggested in the comments already. Anyway, for completeness sake. Maybe someone can merge the answers? Of course it also possible to use python's subprocess, e.g. import subprocess def merge(first, second, out_file): """ This utility will automatically mosaic a set of images. All the images must be in the ...



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