lofreq
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'lofreq' Versions
- 2.1.5
Link to section 'Commands' of 'lofreq' Commands
- lofreq
Link to section 'Module' of 'lofreq' Module
You can load the modules by:
module load biocontainers
module load lofreq
Link to section 'Example job' of 'lofreq' 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 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