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By "marker positions" I mean adding metadata that refers to a specific time in the audio.

I could add an outline of the audio in the metadata comments, but that's technically just normal text, which isn't what I want to do.

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What you are talking about are often referred to as cue points. These markers are saved in a "cue sheet" which is a separate file that contains them. These cue sheets are recognized by several audio players.

You don't mention what format you want to add marker positions - and the only format that I know that have them built in are iTunes audio book files. They call them "index markers" and I don't know of any available tools that support them.

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  • BWF store them as well. Pro audio editing apps should read the cue points.
    – Gyan
    Commented Jan 19, 2017 at 5:53
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WAV files support storing cue markers in a chunk type of 'cue '. I know that Adobe's Audition will read and write these. There are other formats that Audition reads which also have marker support.

FFMpeg has added support for wav cue markers, FFmpeg Ticket 8872

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