1. A method of backing up data from a source file system of a computer device to a backup data storage system, the method comprising: checking whether a source file is locally stored on the source file system in a local deduplicated format of the source file system; when the checking indicates that the source file is stored in the local deduplicated format, then— determining a block size value used to store the source file in the deduplicated format; accessing, without a file read/write assistance from an operating system running on the computer device, a local deduplication database to determine a location of a first data chunk of the source file stored in the deduplicated format on a local storage device; and, backing up the source file by accessing and selectively transferring the first data chunk and successive data chunks of the source file by: transferring a given data chunk, if the local deduplication database indicates that the given data chunk was not deduplicated; and transferring a deduplication record, without transferring the given data chunk, if the local deduplication database indicates that the given data chunk was deduplicated; and when the check indicates that the source file is locally stored without deduplication on the computer device, then backing up the source file by transferring data chunks of the source file to the backup data storage system and performing deduplication on the data chunks of the source file.