vgteam
Identifying SV type with vg call
1. What were you trying to do?
I would like to identify structural variant (SV) type (e.g., <INS>, <DEL>, etc.) as part of the vg call step on a gam created by aligning short-reads with vg giraffe to a minigraph-cactus graph.
2. What did you want to happen?
Identification of the SV type either in the ALT or other VCF field.
3. What actually happened?
The vg call produced VCF does include useful information in the ALT field but I would like to do a comparison of SVs called with vg vs. other, linear-reference based approaches. This doesn't seem possible without these symbol fields.
4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
5. What data and command can the vg dev team use to make the problem happen?
I am using vg call on a graph produced with minigraph-cactus. I have pre-computed snarls.
6. What does running vg version say?
vg version v1.49.0 "Peschici"
Compiled with g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 on Linux
Linked against libstd++ 20220421
Built by anovak@octagon
Hi, did you find a solution to this, because I am struggling with this as well. I do not understand how exactly one is to deduce the SV types from the vcf files. I succeeded getting VCF calls from vg call to my read alignment for my graph, but I do not have any clue of how to get the SV types (DEL, INS, etc). Thanks and cheers.
Hello, I have the same question. I am considering taking a deep dive into the VCF produced by pggb with vg call, and am eager to get some guidance. I'll report here if I make progresses.
