Question: passing a third-party GFA to vg tools
0
gravatar for egoltsman
6 months ago by
egoltsman0
United States
egoltsman0 wrote:

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

vg • 221 views
ADD COMMENTlink modified 5 months ago • written 6 months ago by egoltsman0
1

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

ADD REPLYlink written 5 months ago by glenn.hickey170
0
gravatar for egoltsman
5 months ago by
egoltsman0
United States
egoltsman0 wrote:

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!

ADD COMMENTlink modified 5 months ago • written 5 months ago by egoltsman0
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