Question: GAF format from vg
0
gravatar for colindaven
3 months ago by
colindaven2.5k
Hannover Medical School
colindaven2.5k wrote:

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

vg assembly • 245 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by colindaven2.5k
1
gravatar for colindaven
3 months ago by
colindaven2.5k
Hannover Medical School
colindaven2.5k wrote:

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

ADD COMMENTlink written 3 months ago by colindaven2.5k

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

ADD REPLYlink written 3 months ago by genomax92k

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.

ADD REPLYlink written 3 months ago by glenn.hickey160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1648 users visited in the last hour