Purdue University

Commands

• smoove

Module

You can load the modules by:

module load biocontainers
module load smoove

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 Smoove on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=smoove
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers smoove

smoove call \
    -x --name my-cohort \
    --exclude hg38_blacklist.bed \
    --fasta  Homo_sapiens.GRCh38.dna.primary_assembly.fa \
     -p 24 \
    --genotype input_bams/*.bam