Vg

Introduction

Variation graphs (vg) provides tools for working with genome variation graphs.

For more information, please check:

Quay.io: https://quay.io/repository/vgteam/vg?tabinfo | Home page: https://github.com/vgteam/vg

Versions

• 1.40.0

Commands

• vg

Module

You can load the modules by:

module load biocontainers
module load vg

Example job

Warning

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