Lofreq

Introduction

Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.

For more information, please check its website: https://biocontainers.pro/tools/lofreq and its home page on Github.

Versions

• 2.1.5

Commands

• lofreq

Module

You can load the modules by:

module load biocontainers
module load lofreq

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 Lofreq on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=lofreq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers lofreq

lofreq  call -f ref.fa -o vars.vcf out_sorted.bam

lofreq call-parallel --pp-threads 8 \
     -f ref.fa -o vars_pallel.vcf out_sorted.bam