The Bam format was developed at a time when I/O (disk / network) was not a limiting factor for genomics data analysis. Currently it is. Especially when you have pipelines like GATK that process BAM files in multiple steps and read and write bam files for every step (instead of in memory streaming).

I know raw sequencing data (SOLiD & PacBio) and other large (scientific, financial etc.) datasets are stored in [HDF5](http://www.hdfgroup.org/HDF5/). And there are initiatives like [CRAM](http://www.ebi.ac.uk/ena/about/cram_toolkit) and [reduced bam](https://www.broadinstitute.org/gatk//events/2038/GATKwh0-BP-4-Compression.pdf).

Still I believe most organizations are using regular bam files. Why is this? Is there a roadmap towards development (and adoption!) of improved formats for storing DNA alignment data?
> Why is this?

because, most tools (samtool 0.1.19), workflows... still use BAM.

you never change a winning team.

HDF5: I don't think it's the best tool to store data (you want Streaming , you want to avoid padding of data if the record is tool small, you want bgzip compression,... ). On a personnal side, I think HDF5 is a nightmare to program in C. https://www.biostars.org/p/69/

oh and why don't people use XML or JSON instead of VCF? why don't people all use the same best programming language (which is java *) :-)

(*) troll.