Harshvardhini yes there will be a separate merit list will be made for girls in JEE Advanced 2018. But this list does not work the way you must be thinking. First of all the girls who are in the top general merit list and got admission into an IIT will be excluded from the list then it will be checked that how much percentage of girls are there in every IIT. It is mandatory now to have 14% girls in each IIT. If all the IITs have 14% or more than this percentage of girls then no extra seat will be added in any of the IIT and no extra girl will be getting admission. But if any of the IIT has less than 14% of the girls then the extra number of seats will be added in the IIT to complete the figure and the girls from the separate merit list will be given admission according to their preference list. 

This strategy is made to increase the gender diversity in the IITs without snatching the seat from any boy who deserved to get admission in the IIT.

Feel free to ask if you have any more queries. All the best!!