wiggletools sum [bigwig files...]
The sum function from wiggletools takes an arbitrary number of bigwig files as input, sum up (or merge) the signal values, and write the result in wig format to stdout. The file list is separated by spaces and terminated by a colon (:) separated by spaces from other words. At the very end of a command string, the colon can be omitted.
Sum up three bigwig files and write the out put to a wig file called merged.wig:
wiggletools sum test/fixedStep.bw test/variableStep.bw > merged.wig