survivor
Link to section 'Introduction' of 'survivor' Introduction
SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
BioContainers: https://biocontainers.pro/tools/survivor
Home page: https://github.com/fritzsedlazeck/SURVIVOR
Link to section 'Versions' of 'survivor' Versions
- 1.0.7
Link to section 'Commands' of 'survivor' Commands
- SURVIVOR
Link to section 'Module' of 'survivor' Module
You can load the modules by:
module load biocontainers
module load survivor
Link to section 'Example job' of 'survivor' 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 survivor on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=survivor
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers survivor
SURVIVOR simSV parameter_file
SURVIVOR simSV ref.fa parameter_file 0.1 0 simulated
SURVIVOR eval caller.vcf simulated.bed 10 eval_res