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.

References:

• http://bioinformatics.oxfordjournals.org/content/25/21/2865.full.pdf

• http://gmt.genome.wustl.edu/packages/pindel/

• Module Name: pindel (see the modules page for more information)
• environment variables set to /data/$USER/pindeltempdir
  • TMPDIR
• Example files in /usr/local/apps/pindel/TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pindel
[user@cn3144 ~]$ cd /data/$USER/; cp ${PINDEL_TEST_DATA:-none}/* .
[user@cn3144 ~]$ pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load pindel
pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL
cd dir2; pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

cd dir3; pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module pindel