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Guides / Apps for encoding
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With ffmpeg
ffmpeg uses a sectioned parameter approach. Input parameters and input, optionally multiple, output parameters and output target.
In my example I specified copy as codec so the streams are copied as-is, without reencoding. I used map to map video streams 1 and 2 of the first input, and default/all audio streams.
The ffmpeg reference docs are thorough. The wiki has some more guide, example, and explanatory docs.