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Occasionally, I need to manipulate an mkv container (video file). The tool I use is the mkvmerge GUI. This is in the Fedora repository, and you can get it by installing the mkvtoolnix and mkvtoolnix-gui packages. It's probably available for most major distributions.

Some common tasks I've encountered:

Add sub/idx subtitles as a selectable channel. If you have an mkv video and separate sub/idx subtitles, you can add the subtitles to the mkv so they can be turned on/off during playback in your video player. If you're starting with your video in a different container, like avi, first use Handbrake to convert the file. Once you have an mkv, click the 'add' button on the top right and select your mkv video file. Then click 'add' again, and select your idx file. Click 'Start muxing' at the bottom, and in a few seconds the combined file will be ready. Note that this copies the video and audio channels; no encode is occurring so it's very fast. You can now get rid of the original video file and the separate sub and idx files.

Join multiple mkv video files into a single mkv. Sometimes when downloading files, you'll have a two (or more) part video which has been split to allow them to be burned on small media (like CDROM). If you're keeping the file on your hard drive, you can re-join them into a single file. To do this, click the 'add' button on the top right and select your first mkv video file. Then click 'append' (not add), and select the second mkv video file. Click 'Start muxing' at the bottom. Again, this is just a copy operation, so it's very fast. You can now get rid of the original video files.
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