NCO:ncap2 is the function to do it: ncap2 -s 'new_var=var1+var2' in_filename.nc out_filename.nc The output file will have all of the variables that exist in the input file as well as the new_var. Add -O if your input and output files are the same (overwrite). I do not know what the -s stands for. BUT the new_var will have the same long_name as the first variable used for summing (i.e. it could make some things a bit confusing).
The NCO (netCDF Operator) command ncks (netCDF Kitchen Sink). From the documentation: The nickname “kitchen sink” is a catch-all because ncks combines most features of ncdump and nccopy with extra features to extract, hyperslab, multi-slab, sub-set, and translate into one versatile utility. ncks extracts (a subset of the) data from input-file and and writes (or pastes) it in netCDF format to output-file, and optionally writes it in flat binary format to binary-file, and optionally prints it to screen.
NCO:ncap2 and .total ncap2 -s 'summed_variable=variable_to_sum.total($lat,$lon)' in.nc out.nc Make sure to use single quotes. If your in.nc==out.cnc then adding -A will save you from having to specify “overwrite” (see this). ncap2 -A -s 'summed_variable=variable_to_sum.total($lat,$lon)' in.nc out.nc