I've got a JVC HD camcorder which uses a proprietary MTS container. It is however quite simple to re-mux those videos into MKV (without re-encoding, which is also possible but of course much slower):
ffmpeg -i input.mt2s -scodec copy -acodec copy -vcodec copy -f matroska input.mkv
An a bash script to automate that:
#!/bin/bash
# m2tstomkv_subs (Fix the faulty fps (dual frames in the interlaced fields with same time-stamps) and repackage in matroska mkv container)
time {
# remux m2ts movies into mkv with ffmpeg
for i in *.m2ts; do
ffmpeg -i $i -scodec copy -acodec copy -vcodec copy -f matroska `basename $i .m2ts`.mkv;
echo "Conversion done";
done
}
exit;