gridss
Link to section 'Introduction' of 'gridss' Introduction
Gridss is a module software suite containing tools useful for the detection of genomic rearrangements.
Docker hub: https://hub.docker.com/r/gridss/gridss and its home page on Github.
Link to section 'Versions' of 'gridss' Versions
- 2.13.2
Link to section 'Commands' of 'gridss' Commands
- R
- Rscript
- gridss
- gridss_annotate_vcf_kraken2
- gridss_annotate_vcf_repeatmasker
- gridss_extract_overlapping_fragments
- gridss_somatic_filter
- gridsstools
- virusbreakend
- virusbreakend-build
Link to section 'Module' of 'gridss' Module
You can load the modules by:
module load biocontainers
module load gridss
Link to section 'Example job' of 'gridss' 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 Gridss on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gridss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers gridss