FFmpeg kindly provides a straightforward way can create master HLS playlist. You can simply do it by adding master_pl_name as a part of ffmpeg encoding options. Make sure to require a closed GOP when encoding and to set the GOP size to fit your segment time constraint. For more information, please refer at https://ffmpeg.org/ffmpeg-formats.html#hls

Following example shows how to create a master HLS playlist.m3u8 by combination of 

ffmpeg -i in.ts -b:v:0 1000k -b:v:1 256k -b:a:0 64k -b:a:1 32k \
-map 0:v -map 0:a -map 0:v -map 0:a -f hls -var_stream_map "v:0,a:0 v:1,a:1" \
-hls_segment_filename 'file_%v_%03d.ts' out_%v.m3u8

If you are considering fragmented MP4, the option you need to add is just adding -hls_segment_type fmp4.

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