BibTool can be used to extract the references used in a document. For this purpose BibTool analyzes the .aux file and takes the information given there. This includes the names of the BibTeX files. Thus no BibTeX files have to be given in the command line. Instead the .aux file has to specified --- preceded by the option -x.

bibtool -x document.aux -o document.bib

The second option -o followed by a file name specifies the destination of the output. This means, instead of writing the result to the standard output stream the result is written into this file.

BibTool Manual Introduction Using BibTool --- Some Instructive Examples Extracting Entries for a Document