MeGUI is an x264 front end and VirtualDub is meant for capture and processing video, which also means it can encode. Point being, they're both meant to encode
video, not decode. If you need to deinterlace the video as part of the encode process, you need look into AviSynth and the various filters it includes/supports. For deinterlacing, I would suggest NNEDI
. Alternatively, there are various GUI based encoders like Handbrake that can do it for you.