Hello Ketan,
Yes, you will be able to get admission in IITs after attempting either EE or EC paper. You can opt for any of the two paper. Since you are from B.Tech- EEE branch, you should attempt the same paper in GATE as well.

You can go through the following link to know the details regarding the cutoff of GATE 2018 by IIT Delhi for admission into M.Tech-VLSI programme.

Link: http://vdtt.iitd.ac.in/MENU/Admissions/Short-listed_criteria.pdf

Please feel free to comment below for further assistance.

All the best!