Is it possible to embed VTT subtitles & chapters in webm video?
Edit: It seems that WebM now supports VTT subtitles. See the link below for detailed information.
If you want to add subtitles to a video on a web page, have a look at the HTML5 'track' element. It allows adding subtitles without muxing them into the video container. More details here: https://developer.mozilla.org/en-US/docs/Web/Apps/Fundamentals/Audio_and_video_delivery/Adding_captions_and_subtitles_to_HTML5_video

WebM doesn't support subtitles nor chapters right now so you won't be able to embed them without creating a WebM file that is out of specs.
You will probably want to remux your video into mkv and then convert your VTT subtitles to SRT and mux these into your mkv aswell.

From http://www.webmproject.org/docs/container/


  Initial WebM release does not support subtitles.
  
  WHATWG / W3C RFC will release guidance on subtitles and other overlays in HTML5  in the near future. WebM intends to follow
  that guidance. Ref: WebVTT.