Software: Pindel
Description
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.
Available Versions
| Unspecified: | 0.2.5b9 |
|---|
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.
Commands
- pindel
- pindel2cvf
Module
You can load the modules by:
module load biocontainers
module load pindel
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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