Extract a single chromosome or a region of the chromosome from GBZ

[jikhashkya]

Hi,

I have a GBZ file from Minimap-cactus and I want to extract a single chromosome or a region of the chromosome as a way to subset the GBZ graph. Is it possible to do this directly using GBZ as the input graph? I looked into vg chunk and vg find but I didn't see any flags that explicitly supported extracting a chromosome or a region of the chromosome. The best I could do was run the following command:
vg chunk -x <input>.gbz -S <input>.snarl -p GRCh38#0#chr20:2000000-3000000 -O gfa > subgraph.gfa. I assume this provides the snarl in the chr20 in the given base pair range.

Any pointers to the proper documentation or tutorials would be greatly appreciated. I looked through the wiki but it didn't necessarily help so I apologize if I missed something obvious.

Thank you.

[xchang1]

Hi,

Your command looks right to me. Is it giving you an unexpected output?

If you want the path and all the nested variants too, then I think your command is right. Using the snarls can be a bit slow though.
If you're only interested in the path and the stuff close to it, you can use --context-steps or --context-length to walk out from the nodes along the path.
If you want the whole chromosome, you can use the --components flag that will give you the whole connected component.

[jikhashkya]

It was giving the expected output however I just wanted to get a region without the snarl. When I tried to run the command with only -p flag, it requires me to use the flag with either -S or -c flags.
Thank you for your clarification. I think that kind of answers my question. Just to confirm, to extract a single chromosome's subgraph from the graph, I can run something like vg chunk -x <input>.gbz --components -p GRCh38#0#chr20 -O gfa > subgraph.gfa ?

Now, is there a way to filter the reads that are mapped within a certain region? For instance, if i have alig.gam file that was obtained from giraffe, and I want to only extract the reads that are mapped between node A and node B of the graph?

And is there a way to chunk the graph so that the haplotype paths are retained in the subgraph?