I can remember where I read it but, I recall that I have read some where that if you have a bam sorted, you can unsorted it and some programs don't change the header (was samtools? picard?) so the SO:coordinate still is there. Is that true? Could I be sure that a file is sorted only looking to the bam header SO tag? or should I need always double check sorting them with samtools sort?.
Which is your preferred way of checking that the bam files passed to you are really sorted?