Dear aspirant,
It's a bit complicated as you are doing an integrated degree .
Th ere is one problem you should have a valid gate score card and without this you won't be able to take admission in the IITs . You also need to score a minimum of 60% in your mtech.
For example in admission into IIT Roorkee in PhD programme check out this link for all the details-
https://engineering.careers360.com/news/phd-iit-rourkee
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