Visualizing Graph Alignment Format via minigraph

Question

[ivazirabad]

Hello,

I am new to using genomic graphs vs linear references, so I have a question about the output formats and understanding more about what can be done with them. I have a whole genome FASTA, and I used minigraph to map this FASTA to a pangenome graph, producing a file in GAF format. What can I do to further analyze the file, or visualize it? I don't see anything online about how the GAF format can be further utilized.

Answer 1

[colindaven]

That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like format) by mapping quality etc. You can't call SNPs, but you probably already called SVs with gfatools, correct ?

I've tried to record info about pangenomics file formats here: https://github.com/colindaven/awesome-pangenomes

Keep in mind the rgfa ecosystem (minigraph) isn't really compatible with the GFA ecosystem (vg, odgi etc ).

[colindaven]

New to me : you can view the rGFA reference GFA format from minigraph output with this tool:

https://github.com/codeatcg/VRPG