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