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tools for working with genome variation graphs
In https://github.com/ekg/freebayes/issues/419 @tseemann [asked if vg was ready for bacterial pangenomics](https://github.com/ekg/freebayes/issues/419#issuecomment-377646948). My response better fits here so I've copied it over: @tseemann you already can use vg on large pools...
This is a bit of a winding journey to try and solve #3126 , so hopefully haven't missed out too many details. I'm using a minigraph GFA as input (so...
**1. What were you trying to do?** Call variants from read support. **2. What did you want to happen?** Generate a VCF file. **3. What actually happened?** The command have...
**1. What were you trying to do?** Try to genotype SVs from the short-reads ''' vg map -t 6 -f Pyc_us5_1.fastq.gz -f Pyc_us5_2.fastq.gz -x wg.xg -g wg.gcsa > wg_test.gam vg...
**1. What were you trying to do?** I was trying to use vg mcmc to infer haplotypes from a mgam file. **2. What did you want to happen?** I wanted...
I'm using vg construct to construct a linear graph here is the command : vg construct -r genomes/AE005174.2.fa > x.vg here is the warning: warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found...
**1. What were you trying to do?** I was trying to performe the augmentation step before variant calling to call variants from a set of illumina WGS reads that I've...
xxd isn't installed in the test container for vg CI, but the surject tests need it. But they also don't fail without it; they just complain and don't actually check...
**1. What were you trying to do?** Call variants with vg. I'm trying to align of paired-end illumina reads from different bird individuals to a vg graph generated with the...
Asking for the Debian-Med team, @tillea found https://doi.org/10.1038/nbt.4227 but I wanted to double check
