delly
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'delly' Versions
- 0.9.1
- 1.0.3
- 1.1.3
- 1.1.5
- 1.1.6
Link to section 'Commands' of 'delly' Commands
- delly
Link to section 'Module' of 'delly' Module
You can load the modules by:
module load biocontainers
module load delly
Link to section 'Example job' of 'delly' Example job
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