vg
Link to section 'Introduction' of 'vg' Introduction
Variation graphs (vg) provides tools for working with genome variation graphs.
Home page: https://github.com/vgteam/vg
Link to section 'Versions' of 'vg' Versions
- 1.40.0
Link to section 'Commands' of 'vg' Commands
- vg
Link to section 'Module' of 'vg' Module
You can load the modules by:
module load biocontainers
module load vg
Link to section 'Example job' of 'vg' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run vg on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vg
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers vg
vg construct -r test/small/x.fa -v test/small/x.vcf.gz >x.vg
# GFA output
vg view x.vg >x.gfa
# dot output suitable for graphviz
vg view -d x.vg >x.dot
# And if you have a GAM file
cp small/x-s1337-n1.gam x.gam
# json version of binary alignments
vg view -a x.gam >x.json
vg align -s CTACTGACAGCAGAAGTTTGCTGTGAAGATTAAATTAGGTGATGCTTG x.vg