How do I transfer MKV file from Windows PC to iPad Mini? I have installed iTunes on Windows PC but I can't any option to transfer file.
Do not bother with conversion. Install the free video players like VLC or PlayerXtreme and upload the videos via wifi directly to the apps.
EDIT: Alternatively, and also must faster for large files, both apps allow transfers via iTunes. If you don't use iTunes read on...
For example, once installed you enable Wifi Transfers...
Then from your browser you go to the address shown and upload the files...
Look at it as a multi-step approach
Convert your MKV video into an MP4/M4V which the iPad can play. On OS X there is software like Handbrake for this, I'm sure there are similar applications available on Windows.
Import the converted video into iTunes
Use iTunes to sync the video to your iPad
If you have troubles with one of these steps, there are various questions with answers for each of them on this site already. In case you can't find them, don't hesitate to ask a new question.