Skipping commercials when using video viewer like VLC?

The skipping commercials feature works flawlessly for me in Channels ATV.
But is there a way to use those markers in the video file while playing in another application like VLC?

My DVR records .mpg files from HDHomerun Prime to local drive on an iMac.

I would like to be able to view those files on my iMac using a video player like VLC and skip the commercials.

The video markers are part of the metadata of the video in our database. They are not embedded into the video file.

Gotchya. Thanks for clarifying.