vg call - Selecting reference path to call on

Question

[AshleeThomson]

Hi guys

A quick and silly question. I'm using vg call to detect variants in data that I've mapped to a graph, but I'm wanting to define which reference paths I call on. I can see how this is done:

-p, --ref-path NAME     Reference path to call on (multipile allowed.  defaults to all paths)

But I'm wondering what format you define the multiple paths. Is it just a string (1 2 3 4) or comma separated (1,2,3,4) or can you indicate a file containing the select paths (paths.txt).

Thanks in advance.

[Simon]

I am trying to use this option, however it says error [vg call]: Reference path "REF#PATH" not found in graph. I then went back to convert the GBZ to GFA. And indeed all my reference paths are missing. So it must be a vg autoindex problem. I am running vg autoindex -p PREFIX -w giraffe -g INPUT_GRAPH.gfa -t 28 -r ALL_REF_SEQUENCS.fa. I don't see any other option in vg autoindex to tell it my reference paths. The graph was constructed with PGGB. Any help highly appreciated!

[Simon]

Reading into https://github.com/vgteam/vg/wiki/Path-Metadata-Model#data-model I have an idea of what is going wrong: The naming of my sequences. I thought VG would respect the https://github.com/pangenome/PanSN-spec naming scheme, but apparently for reference sequences, this is different. A reference-biased naming scheme xD

Will report back if this solved my issue.

[Ram]

I moved your post to a comment, but I have a question for you - why did you add it as an answer in the first place?

[Simon]

This is the first time I am using Biostars and I failed miserably, sorry!

[Ram]

Genuine mistakes are not miserable failures, please take it easy. In the future, please only add answers if you're answering the top level question. Otherwise, use Add Comment or Add Reply as appropriate.

Answer 1

[Jordan M Eizenga]

When options are marked as multiple allowed in VG, you can specify the option more than once in one CLI invocation. The syntax would be -p chr1 -p chr2, etc.

[AshleeThomson]

Jordan M Eizenga Awesome! Thank you for the clarification. I'll keep that in mind next time I want to use multiple options for other commands too.