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I use a program called Super to do all my video conversions. It will handle these input formats.
3gp, 3g2, amv, asf, avi, dat, dvr-ms, fli, flc, flv, m2ts, mpg, mkv, mov
m4v, mp4, nsv, ogm, qt, rm(vb), str, swf, ts, trp, ty, ty+, tmf, viv, vob, wmv
As long as your input format is one of these it should be able to do what you want.