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tools for working with genome variation graphs
Hi, Vg team, I’m @Sourirewang and I’m interested in vg tools.I just have two full-length transcriptome and many transcriptome sequencing data. And I wonder whether a pantranscriptome can be constructed...
Hi Vg team, I have a problem,I'm wondering if Vg tools can be used for variants(snp;indel;SV) call basing on bulk RNA sequencing. You known that the small variants can be...
Hello, I want to find some examples about the gam file format, because I can't open the gam file, and there are garbled characters when I force it to open....
@adamnovak @jeizenga Hello, i'm getting the same problem when outputting a **BAM file** with ```vg giraffe```, not sure if I should open a new issue ?! please tell me if...
Starting from VCFs that have phased haplotypes, what steps should we follow to build a GFA in which the haplotypes are repressented as paths? It seems that we might be...
Hi, Can vg call SNP or Indel in insertion? like this figure. They used linear pan-genome reference with the insertion included, and they found an SNP present in the insertion....
There is nothing at https://biostars.org/t/vg anymore. Maybe we want https://www.biostars.org/tag/vg/ instead?
Good Morning , i want to know what's the best way to annotate pangenome graphs ? as i've read in litterature, there is no proper way and we're only able...
Hello, I am trying to use a variation genome graph to genotype SVs on more samples sequenced with short-reads, and I'm trying different avenues (see 1)graph from vcf + giraffe...
Hi all, I would like to know if anyone has ideas on how should I get the SV types (INS/DEL/INV) from the output vcf of minigraph>cactus>vg-giraffe>vg-call pipeline. Are there any...
