gridss.rst

Gridss

Introduction ~~~~~~~~ Gridss is a module software suite containing tools useful for the detection of genomic rearrangements.

For more information, please check its | Docker hub: https://hub.docker.com/r/gridss/gridss and its home page on Github.

Versions

• 2.13.2

Commands ~~~~~~~ - R - Rscript - gridss - gridss_annotate_vcf_kraken2 - gridss_annotate_vcf_repeatmasker - gridss_extract_overlapping_fragments - gridss_somatic_filter - gridsstools - virusbreakend - virusbreakend-build

Module

You can load the modules by:

module load biocontainers
module load gridss

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 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