I'm trying to extract a section of a raster file that overlaps with a polygon shapefile in QGIS 2.18.3. When I run extract, I'm left with a large null value area as part of the extent of the output raster.
And the raster (.tif) which had this large null value area since the first time I clipped one of two DEMs that were merged together to create this layer:
I used Raster -> Extraction -> Clipper tool with the .tif input and .shp mask layer shown above, and it produced this output:
Using clipping option "Crop the extent of the target dataset to the extent of the cutline" didn't do much better:
Here are the settings I'm using in QGIS' clipping tool:
How do I get the DEM clipped exactly to the boundaries of the shapefile of interest in QGIS? Open to recommendations of other open source GIS tools as well but would prefer using this since I'm already up and running and learning my way around it.