I am working in an interdisciplinary area and most of my area specific journals are available in journal which are indexed by SSCI instead of SCI. But some people told that for computer science resaerchers SCI is preferred one. What should I do ? I have an option where I could publish in SCI journal which have much less IF as comapred to that of available SSCI indexed journals
This strongly depends on each particular country's bureaucracy, and on your planned career path. Unfortunately I don't think there is a single answer, but rather you will need to look at the requirements of the specific grants you will be requesting, specific positions you will be applying for, etc.
For example, I'm in a similar position as you and located in Spain. I need to publish in SCI journals for my promotion and tenure applications, because here if you are at a science department SCI is king and the rest counts practically zero for those purposes. However, when applying for a project grant I have been successful going to a non-CS panel and highlighting my publications in non-CS venues, and when applying for EU funding I have been successful highlighting good conference papers in my subfield (which is really where the most relevant publications are) and not even mentioning SCI. Americans in my field go straight to conferences and not even bother with SCI, Chinese do publish in SCI because it seems to be a requirement there, some offers for positions I have seen in northern Europe just list a mix of SCI journals, non-SCI journals and conferences that are relevant, etc.