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gdal_merge.py is the correct tool to 'stack' your input images. Assuming that your first band has a valid color table you could use: gdal_merge.py -separate -pct -o output_file.tif file1.tif file2.tif file3.tif Note: The command has been reformatted with -o output_file.tif before the list of inputs. From the docs: -pct: Grab a pseudocolor table ...

The first way I can think of is to build a vrt, edit and translate: gdalbuildvrt -separate output.vrt file1.tif file2.tif file3.tif add the color interp tag where needed: ... <VRTRasterBand dataType="Byte" band="1"> <ColorInterp>Red</ColorInterp> <NoDataValue>255</NoDataValue> <ComplexSource> <SourceFilename ...

I have a solution! It IS because of the old and infuriating GDAL upside-down export to GeoTiff (see my comments above)! Before anybody tells me that this has been fixed - I agree it does appear to be fixed but I was using a mixture of data converted with a older version of GDAL about 4 years ago and data I converted with the latest version of GDAL about 3 ...

While I don't know why GDAL provides this overlap in functionality, be sure to set the cache for gdalwarp to make it really fast: # assuming 3G of cache here: gdalwarp --config GDAL_CACHEMAX 3000 -wm 3000 $(list_of_tiffs) merged.tiff Be sure to not define more cache than having RAM on the machine.

Yes, the two different version of GDAL_merge do behave differently. I ran into a similar problem (see this post), though yours appears to be a little different. Basically, I think that the more recent version is the one to trust. The reason it works differently is because thankfully it has been updated, so it should not be unbelievable.