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.
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AshleeThomson •
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.
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.
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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 avg autoindexproblem. I am runningvg autoindex -p PREFIX -w giraffe -g INPUT_GRAPH.gfa -t 28 -r ALL_REF_SEQUENCS.fa. I don't see any other option invg autoindexto tell it my reference paths. The graph was constructed with PGGB. Any help highly appreciated!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.
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?
This is the first time I am using Biostars and I failed miserably, sorry!
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
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