Purdue University

Commands

• impute2

Module

You can load the modules by:

module load biocontainers
module load impute2

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 Impute2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=impute2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers impute2

impute2 \
    -m Example/example.chr22.map \
    -h Example/example.chr22.1kG.haps \
    -l Example/example.chr22.1kG.legend \
    -g Example/example.chr22.study.gens \
    -strand_g Example/example.chr22.study.strand \
    -int 20.4e6 20.5e6 \
    -Ne 20000 \
    -o example.chr22.one.phased.impute2