Converting HD movie file to Itunes

hi
i have an HD clip in 1020p which i want to convert to an HD format compatible with ATV/iTunes. I understand that ATV will only support 720p. The file itself is an .mkv format.
I have tried with visual hub using preset to Apple TV and selecting hi quality but the file reduced from 10Gb to roughly 2.Gb and appears to be SD. Also Visual Hub didn't offer a format to convert the 1020p to so how would i know if the process i'm using is HD (it took many hours to get where i am now so it would be useful to know the intended output of the conversion). Is Handbrake a better option and if so any quicker?
Any tips advice etc please.

You could try MPEG Streamclip. Select Apple TV then to the right click iTunes and choose the 1280x720 HD option. It can take a very long time depending on the size and .mkv files always seem to take more time than other file formats. I got one I'm converting now and after 42 hours it's only 58% complete the file is just short of 2 hours long

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