delly is an integrated structural variant prediction method that can detect 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.

References:

• Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M. Stuetz, Vladimir Benes, Jan O. Korbel. Delly: structural variant discovery by integrated paired-end and split-read analysis.. Bioinformatics 2012, 28:333-339. Pubmed  |  PMC  |  Journal

• GitHub

• Module Name: delly (see the modules page for more information)
• delly is a multithreaded application. The delly module sets the $OMP_NUM_THREADS environment variable automatically to match $SLURM_CPUS_PER_TASK. However, note that delly primarily parallelizes on the sample level, so there is no benefit to allocating multiple CPUs when processing a single sample.
• Example files in $DELLY_TEST_DATA
• Files with regions to exclude from calling for some genomes can be found in $DELLY_EXCL_FILES

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

[user@biowulf]$ sinteractive --mem=5g
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 delly/0.7.8
[user@cn3144 ~]$ delly
**********************************************************************
Program: Delly
This is free software, and you are welcome to redistribute it under
certain conditions (GPL); for license details use '-l'.
This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'.

Delly (Version: 0.7.8)
Contact: Tobias Rausch (rausch@embl.de)
**********************************************************************

Usage: delly  

Commands:

    call         discover and genotype structural variants
    merge        merge structural variants across VCF/BCF files and within a single VCF/BCF file
    filter       filter somatic or germline structural variants

[user@cn3144 ~]$ cp $DELLY_TEST_DATA/* .
[user@cn3144 ~]$ # calling somatic SVs
[user@cn3144 ~]$ delly call -o test.bcf -g DEL.fa DEL.bam
[...snip...]
[user@cn3144 ~]$ module load samtools
[user@cn3144 ~]$ bcftools view test.bcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20180308
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Translocation">
##ALT=<ID=INS,Description="Insertion">
...

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

Create a batch input file (e.g. delly.sh) similar to the following example:

#! /bin/bash

function die {
    echo "$@" >&2
    exit 1
}

module load delly/0.7.8 || die "Could not load module"
cd /data/$USER/data_for_delly
delly call -o delly_calls.bcf -g ref.fa \
    sample1.bam sample2.bam sample3.bam sample4.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g delly.sh

Loading the module as part of the batch script will automatically set the OMP_NUM_THREADS variable to match the number of allocated CPUs. If not loading the module in the batch script, please set OMP_NUM_THREADS explicitly.

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

export OMP_NUM_THREADS=2; cd /data/$USER/dir1; delly call -o del.bcf -g ref.fa sample1.bam
export OMP_NUM_THREADS=2; cd /data/$USER/dir2; delly call -o del.bcf -g ref.fa sample2.bam
export OMP_NUM_THREADS=2; cd /data/$USER/dir3; delly call -o del.bcf -g ref.fa sample3.bam
export OMP_NUM_THREADS=2; cd /data/$USER/dir4; delly call -o del.bcf -g ref.fa sample4.bam

Submit this job using the swarm command.

swarm -f delly.swarm -g 10 -t 2 --module delly/0.7.8