Pindel

Program description:
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

Versions:

Name: pindel
Version: 0.2.5b8
Platform: x86_64
Category: Applications/Engineering
URL https://github.com/genome/pindel

Below is how to load the module into the software:
Module loading reference

Sample SLURM runtime script:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4gb
#SBATCH --time=01:00:00

# Set paths or load appropriate modules
module load pindle

# Set the $TMPDIR variable
export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID

# Create a temporary directory
mkdir -p ${TMPDIR}

# Copy the input data to the directory pointed to by the $TMPDIR variable
cp ${pidel_root}/demo ${TMPDIR}

# Go to the $TMPDIR directory
cd ${TMPDIR}/demo

# We do the calculations

pindel -i simulated_config.txt -f simulated_reference.fa -o bamtest -c ALL
# pindel -p COLO-829_20-p_ok.txt -f hs_ref_chr20.fa -o colontumor -c 20
# pindel2vcf -r hs_ref_chr20.fa -R HUMAN_G1K_V2 -d 20100101 -p colontumor_D -e 5


# Footer
cat << EOF
-------------------------------------------------- ---------------

End of calculations [$(date)].

-------------------------------------------------- ---------------
EOF

# We finish the calculations, we copy the contents of the $TMPDIR directory
# to the directory from which the job was queued.
cp -r $TMPDIR $SLURM_SUBMIT_DIR

# Clear working directory
rm -rf $TMPDIR

Example input: