Question

SAM @HD VN allowed values

2

Entering edit mode

9.5 years ago

Matt Shirley 10k

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 • 3.8k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by Matt Shirley 10k

Ram · Accepted Answer · 2014-11-24

3

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9.5 years ago

Devon Ryan 104k

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.

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by Devon Ryan 104k

0

Entering edit mode

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!

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by Matt Shirley 10k

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Entering edit mode

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.

ADD REPLY • link 9.5 years ago by Devon Ryan 104k