I'm. Just throwing it out there, but is there a programme that will let me merge multiple video and audio files together in a batch. I would like it to be able to merge one video with one audio file at a time and have them in a queue so that they batch process as I will have a large amount to do (100+).
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Are your files tied together by some naming convention, or will you need to tell the program which files to pair up?
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They will need tying together as they are named differently. Luckily, they won't need to be synced as the audio is the same length as the video.
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Use Mkvtoolnix GUI. Add the files you want to combine, then "Add to job queue". Start the muxing once you have all your jobs ready.
You can make it a bit less annoying by turning some knobs in the settings like "Always use default description when adding a job to the queue" (under "Jobs & jobs queue") and "Clearing settings automatically:" "create new settings" (under "Merge tool") for example.
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