Command-line tool to deduplicate a single humongous file?

I make regular snapshots of my VM using a nightly script. These backups are compressed using WinRAR and do shrink considerably, but I suspect it’s not as efficient as had the file had been deduplicated first (just a hunch which I’m hoping to test).

So instead of compressing the VHD itself, I would like to deduplicate the single file first, and then compress the output of the deduplicator.

Is anyone aware of such a CLI tool?

You can try OpenDedup’s SDFS. It’s not exactly what you’re looking for, but probably as close as you’ll get with Windows.