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tools for working with genome variation graphs
This has annoyed me a few times. I've never bothered to fix but am posting here to remember. I think the safest thing is to just stop using xg's `from_gfa`,...
Hi, I am trying to visualize graph to a base level using `vg viz`: `vg viz -x seqwish.xg -o test.svg` But it gets `Killed` without any error. Thank you for...
https://github.com/vgteam/vg/blob/739f5d7ca589f246fc77574ff77db03d263a6705/src/hts_alignment_emitter.cpp#L132 When we parse a dict file, and a sequence name is missing, we print the whole dict line instead of the sequence name as the sequence we can't find....
I am trying to index a gfa constructed from 3 closely-related melon sequences (to use with `vg map`) using `vg autoindex`. The gfa is ~2G, not particularly large or complex....
Hi, I am trying to add annotation to my graph built using pggb, but I can't seem to see the corresponding paths. I assume I must be doing something wrong....
**1. What were you trying to do?** I was trying to map the following read in vg giraffe (which I have saved in sim.crash.gam, mentioned in section 5 below): ```...
**1. What were you trying to do?** Calling SVs from an augmentation graph. **2. What did you want to happen?** Get novel SVs from the augmentation graph. **3. What actually...
Hi, I want to construct a whole-genome variation graph with vgtools. The reference genome I have contains more than 3,200 scaffolds, and I don't want to abandon them while constructing...
Hello, I have used `giraffe` for alignment using: ``` vg autoindex --workflow giraffe -g chr1.gfa -p pangenome vg giraffe -H pangenome.giraffe.gbwt -g pangenome.gg -mpangenome.min -d pangenome.dist -f sample_R1_paired.fastq.gz -f sample_R2_paired.fastq.gz...
I think this is a more user-friendly alternative to the hotfix that we gave a user in this issue: https://github.com/vgteam/giraffe-sv-paper/issues/4
