Delly2

Description

From the Delly2 Home Page: Delly2 is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.

Version

  • 0.7.2

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Delly2 requires the following module file to run:

  • apps/delly/0.7.2

Running Delly2 on CIRCE/SC

The Delly2 user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for Delly2, and execute the Delly2 binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/delly/0.7.2
[user@wh-520-4-1 ~]$ delly -t DEL -g hg19.fa -v del.sites.vcf -o NA19240.vcf NA19240.bam

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you wish to re-genotype a given SV site list, you would set up a submit script to use delly like this

Single core (Serial) job

#!/bin/bash
#
#SBATCH --job-name=delly-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.delly-test

#### SLURM 1 processor delly test to run for 1 hours.

# Load the delly module:
module load apps/delly/0.7.2

# Start delly
delly -t DEL -g hg19.fa -v del.sites.vcf -o NA19240.vcf NA19240.bam

Multicore job

  • Delly2 primarily parallelizes on the sample level. Hence, OMP_NUM_THREADS should be always smaller or equal to the number of input samples.
#!/bin/bash
#
#SBATCH --job-name=delly-mc-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --output=output.%j.delly-mc-test

#### SLURM 4 processor delly test to run for 1 hours.

# Load the delly module:
module load apps/delly/0.7.2

# Setup number of threads
export OMP_NUM_THREADS=$SLURM_NTASKS_PER_NODE

# Start delly for 4 samples (note number of cores requested)
delly -t DEL -o del.vcf -g ref.fa sample1.sort.bam sample2.sort.bam sample3.sort.bam sample4.sort.bam

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./delly-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Delly2 to the IT Help Desk: rc-help@usf.edu