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tools for working with genome variation graphs
Hi, I tried this command line, but I had this bug. How can I fix this? ``` vg1.40 autoindex -g mouse.parentals.fa.gz.9934a13.417fcdf.53439a3.smooth.final.gfa -t 20 -p mouse.parentals.fa.gz.9934a13.417fcdf.53439a3.smooth.final.autoindex [IndexRegistry]: Checking for haplotype lines...
This changes a (very rare) assertion failure into a (cryptic) message, allowing HG005 to be run on the CHM13-based year-1 HPRC graph. This is probably not the idea fix, but...
I use vg (v1.39.0) construct on a vcf file (VCFv4.2) and hg19 but got the following warning: `"warning:[vg::Constructor] Unsupported variant allele ; Skipping variant(s)"`. After some simple debugging, I find...
Hi All, First off apologies for posting this here, but the Biostars link appears dead. Has anyone tried using Ilummina’s [Polaris SV set](https://github.com/Illumina/Polaris/blob/master/release-data/v2.1/download-instructions.txt) as a graph? We are able to...
**1. What were you trying to do?** I want to 'vg pack' the gam file derived from 'vg giraffe'. An error message appeared. The command line I used is shown...
An unmapped read pair `cat up.gaf`: ``` SRR835033.100738 95 * * * * * * * * * 0 SRR835033.100738 95 * * * * * * * * *...
**1. What were you trying to do?** I am trying to index a GFA graph file (a chromosome) derived from PGGB. **2. What did you want to happen?** index done....
When compiling `vg` from source on macOS, I encountered this unusual `libtool` error message, which I haven't encountered before. ``` glibtool: link: ( cd ".libs" && rm -f "liblogging.la" &&...
I am trying to generate variation graph (vg) from raw SARS-CoV2 sequences (~16k sequences). What would be the best way to generate VCF given these raw sequences? And, does the...
Hello vg team, I have 20 assemblies and a population-scale resequencing data. I want to follow your wonderfull vg Giraffe pipeline to genotype all candidate SVs （INS， DEL， INV）in my...
