Would a specialized cs major (bioinformatics) negatively affect chances for general cs jobs?
I don’t think so in the least! Think about it this way. Programming is one of the few fields where you don’t need to have a degree to land a high-paying job. People these days can get hired on the strength of a GitHub profile alone.
A CS degree is a “feather in your cap”–an added bonus. In our economy today, we pay more for specialization. I would try to use a CS degree in bioinformatics to my advantage in a couple of different ways.
First, when interviewing for a non-bio-specific role, I would point out how rare bioinformatics degrees are compared with the already highly competitive CS degree. Second, I’d do some research and create a list of target companies in the bioinformatics space.
Keep in mind that whatever gaps you think you have on your resume you can fill with GitHub projects, online courses, and boot camp certificates.
I had a CS professor in college who was in charge of the university’s bioinformatics program. He told me that of those applying to the graduate program he preferred biology students to developers. He said, “It’s easier to teach a biologist to code than it is to teach a developer biology.”
Bioinformatics job listings tend to want experience in machine learning and big data. If you can get some practice in these areas with projects and some experience with related technologies (Hadoop, MongDB, and PostgreSQL), you should be in incredibly good shape.