[mfld]

Yes, most bioinformatics tools are the result of research projects.

However, the most common bioinformatics file formats have actually been devised by excellent software engineers (e.g. SAM/BAM, VCF, BED).

I think it is just very convenient to have text-based formats as you don't need any special libraries to read/modify the files and can reach for basic Unix text-processing tools instead. Such modifications are often needed in a research context.

Also, space-efficient file formats (e.g. CRAM) are often within reach once disk space becomes a pressing issue. Now you only need to convince the team to use them. :)