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SAM @HD VN allowed values

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 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.

sam
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updated by Ram Ram • written by Matt Shirley Matt Shirley

1 answer

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.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Ah, okay. This is a sort-of acceptable answer. Since I do use CIGAR operations I'll just version at 1.5. This type of thing should really exist as a comment or table near the appropriate section in the PDF, though. Thanks!

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updated by Ram Ram • written by Matt Shirley Matt Shirley

I left out "new" in front of CIGAR operations!

I think 1.4 added B, = and X. In most cases any version number will work, though most tools don't support the B, = and X CIGAR ops.

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written by Devon Ryan Devon Ryan

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