passing a third-party GFA to vg tools

Question

[egoltsman]

Hi, I'm wondering if it's possible to twist an rGFA formatted graph into a GFA form that vg tools can work with. Heng Li mentions in the minigraph paper that he tried doing that but couldn't get it to work. I guess my chances are slim, but in case some progress has been made since that format came out I'd love to give it a try.

Thank you

[glenn.hickey]

It's something we're working on. I think the main issue is that we only support numeric node ids in vg.

Answer 1

[egoltsman]

I was able to do the conversion after adding the header line, adding paths, and making the segment ids numeric. Since minigraph doesn't trace the sample-path during graph construction, I had to trace them by mapping the assemblies back to the rGFA graph. I think without the paths present in the GFA file vg can't do the conversion.

Thanks!

[colindaven]

Do you have an example repo where you did this exactly ? I'm confronted by the same problem, and your solution sounds challenging and error prone.