GAF format from vg

Question

[colindaven]

Is there a good definition of the GAF format used by the program vg ?

Is this actually GFA format, as perhaps alluded to in this blogpost (not clear) ? https://ekg.github.io/2019/07/09/Untangling-graphical-pangenomics

I would strongly suggest avoiding creating a rival GAF format in bioinformatics, since if you google it you'll find GO annotation file format (see below).

GO Annotation File (GAF) format - Gene Ontology

Thanks

Answer 1

[colindaven]

To answer my own question, here is a good review page by Heng Li. It mentions PAF, GAF, GFA and rGFA.

https://github.com/lh3/gfatools/blob/master/doc/rGFA.md

There is now also a publication here:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02168-z

[GenoMax]

You can accept your own answer in this case to provide closure.

[glenn.hickey]

Yes, it is the GAF as defined on that page that vg outputs. Note that it currently writes the <orientIntv> (as opposed to <stableIntv>) coordinates.