Colour keying was available in FFmpeg since 2.8, but a 'chromakey' filter was included with the recent release of version 3.0. https://twitter.com/oioiiooixiii/status/704052912687878144
# Basic FFmpeg chromakey filter command - see also: 'colorkey' ffmpeg \ -i baselayer.mkv \ -i overlay.mkv \ -filter_complex \ "[1:v]chromakey=green:0.1:0.5[keyed];\ [0:v][keyed]overlay[out]" \ -map "[out]" \ output.mkv
100 layers of "Filthy Frank"
info: https://ffmpeg.org/ffmpeg-filters.html#chromakey
further info: https://ffmpeg.org/ffmpeg-filters.html#colorkey
source video: http://www.filthyfrank.net/