I have around 1200 tiff files (example below), and corresponding .tfw files and .aux files with sonar data that I'd need to merge into one file and I'm struggling to do so.

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I browsed some topics about that problem but doing it manually is just not an option in this case and none of the other solutions helps my case.

Does anyone know if QGIS is capable of merging tiff files and ignoring the white color (i.e. treat it as transparent)?

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    Build virtual raster i QGIS, export as tiff. Or create a Mosaic Dataset in ArcGIS, export. What have you tried? – BERA Jan 15 at 12:19

With QGIS you can use GDAL tool: Raster > Micellaneous > Merge

I was unable to merge many rasters using Merge within QGIS (think there is a limit on number of rasters) but following this instructions worked without problems.

Other option is Virtual raster builder plugin. If you use a lot of rasters might seem like its hanging but it will do the job if you let it work (if you check Task manager, processes you can see its working).

There are also good tools for same task in ArcGis. There you should look into Raster Catalog, Raster Dataset and Mosaic Dataset. More details about it: Differences between Raster Dataset, Raster Catalog, and Raster Mosaic.

If you decide to do it in QGIS I also recommend reading on Handling Many Raster Files in QGIS.

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