Purdue University

Commands

• bamstats.py
• cnx.py
• ftx.py
• guess-ploidy.py
• hap.py
• ovc.py
• plot-roh.py
• pre.py
• qfy.py
• som.py
• varfilter.py

Module

You can load the modules by:

module load biocontainers
module load hap.py

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 hap.py on our clusters:

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

module --force purge
ml biocontainers hap.py

hap.py  \
  example/happy/PG_NA12878_chr21.vcf.gz \
  example/happy/NA12878_chr21.vcf.gz \
  -f example/happy/PG_Conf_chr21.bed.gz \
  -r example/chr21.fa \
  -o test