Pindel

Introduction

Pindel is used to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data.

For more information, please check its website: https://biocontainers.pro/tools/pindel and its home page: http://gmt.genome.wustl.edu/packages/pindel/index.html.

Versions

  • 0.2.5b9

Commands

  • pindel

  • pindel2cvf

Module

You can load the modules by:

module load biocontainers
module load pindel

Example job

Warning

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 Pindel on our clusters:

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

module --force purge
ml biocontainers pindel

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