Snippy
Introduction
Snippy
is a tool for rapid haploid variant calling and core genome alignment.
For more information, please check its | Docker hub: https://hub.docker.com/r/staphb/snippy and its home page on Github.
Versions
4.6.0
Commands
snippy
snippy-clean_full_aln
snippy-core
snippy-multi
snippy-vcf_extract_subs
snippy-vcf_report
snippy-vcf_to_tab
Module
You can load the modules by:
module load biocontainers
module load snippy
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 Snippy on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=snippy
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers snippy