BWA MEM Supplementary Tag Position (0 or 1 based)

Question

[QVINTVS_FABIVS_MAXIMVS]

Quick question.

When I'm viewing the SA tag positions in SAM format. Are the positions 1-based? I think they are, but I can't find any documentation that supports my claim.

Thanks.

[Devon Ryan]

Have you just looked at a supplementary alignment? That would immediately determine this. Having said that, it would be nice if this were clarified in the specs.

Edit: I've asked for a formal clarification.

[QVINTVS_FABIVS_MAXIMVS]

I'm almost certain it is 1 based based on the SA tag and when I look at the split read on IGV. But I wanted a formal clarification. thanks for making an issue.

[John Marshall]

It is indeed a 1-based coordinate, and this has now been clarified in the spec. Thanks for bringing this to our attention.