Hello Anand,

            According to the eligibility criteria specified by the NTA, you need to have passing marks in your respective board. Although to get admission into NITs/IIITs etc., you need to have a minimum of 75% in your boards (for general category), and 65% (for SC/ST category). With 50% in 12th boards, you won't be eligible foe admission into NITs/IIITs, etc. if you don't come in top 20 percentile of your respective board. You can re-appear for JEE Mains and give improvement exams for your 12th boards. 

Best Wishes!