I have a lof of bam files (nearly 500) each 10GB. In total my data occupies 7T. I know bam files are already compressed. Does it make sense to compress the ones I do not use as one unique tgz file? Or any other format?
CRAM generation is actually faster than BAM generation in samtools, at least at the default compression levels. CRAM decoding is slower than BAM though unless you're I/O bound, in which case CRAM will be faster due to being smaller.
For archival, you have to be certain the reference will be around for as long as the archive too. Either cache a copy of it with your files or use the embedded reference mode of CRAM. You can do this with