Annotate GFA with coverage depth

Question

[elcortegano]

I want to visualize a GFA graph in Bandage using the depth node labels. I have noted that this information is absent in the GFA produced by default by vg, e.g.:

vg view graph.vg > graph.gfa

I know the tool vg depth can generate this information:

vg depth graph.vg > draph.depth.tsv

However, it is unclear to me how to use this information to "annotate" the graph, and then how to export everything to a GFA for Bandage. Anybody with experience on this here?

Answer 1

[Jordan M Eizenga]

You can annotate Bandage visualizations using a CSV with a certain structure, so you can process the vg depth TSV into Bandage's expected format and then load it in File > Load CSV data. The format of the CSV is described here: https://github.com/rrwick/Bandage/wiki/CSV-labels

[elcortegano]

Thanks, I can see how generating this CSV file could solve the issue. I only wish there was a more straightforward way to associate the names returned by vg depth (e.g., "15-15_I-5_f4470#1#h1tg000013l#0 6592161") with the actual node names in the GFA (e.g. "14903809").