Can anyone explain what the allowed values for the SAM header (@HD) VN tag are, and what they imply? For example, the [current specification PDF][1] shows:

    @HD VN:1.5 SO:coordinate

What is implied by stating your SAM file is versioned at "1.5", and do any tools actually care about this value? I'm asking because I was about to create an unaligned SAM file from scratch, and am at a loss about how to responsibly set this value.

 [1]: http://samtools.github.io/hts-specs/SAMv1.pdf
Ah the joys of undocumented things. For what it's worth, most tools completely ignore the version number (samtools sort will even just use VN:1.3 if none is specified in the file). I think the only one to watch out for is 1.4 and later, since that added CIGAR operations...though almost no one uses them.