Delly

Introduction

Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.

For more information, please check its website: https://biocontainers.pro/tools/delly and its home page on Github.

Versions

• 0.9.1

• 1.0.3

• 1.1.3

• 1.1.5

• 1.1.6

Commands

• delly

Module

You can load the modules by:

module load biocontainers
module load delly

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 Delly on our clusters:

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

module --force purge
ml biocontainers delly

delly call -x hg19.excl -o delly.bcf -g hg19.fa input.bam
delly filter -f somatic -o t1.pre.bcf -s samples.tsv t1.bcf