How can I get the sequence a line W in GFA is referencing?

[syresbr]

Hi, I used the Cactus-Minigraph to generate a pan-genome of sugar-cane and I would like to get the sequence present in the line W in the GFA to understand the genes presents there. How can I use it?

Other thing, how can I see what parts of the pan-genome are core, acessory and exclusive? I made a script in python to see the number of segments present in each genome and by that define if the line W is core, acessory or exclusive, but I think there might be a better way to do it.

Thanks for your time.

[glennhickey]

You can use vg paths -F to extract paths in the graph as FASTA sequences.

You can use vg depth (maybe binning with -b) to get the number of paths covering each position in the graph, which may help with your second question. Otherwise there may be something in odgi. I agree we should ship easier scripts for this type of analysis.