Hi Shubham,
Yes you can opt for direct Ph.D program in JNU. Refer this link: https://www.jnu.ac.in/csmch-direct-phd . It directs you to appear for JUNEE. You need to apply online. For more information regarding fees, application form you can refer this link:
https://jnuexams.nta.nic.in/Webinfo/Handler/FileHandler.ashx?i=File&ii=292&iii=Y
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