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.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/survivor

Home page: https://github.com/fritzsedlazeck/SURVIVOR

Versions

• 1.0.7

Commands

• SURVIVOR

Module

You can load the modules by:

module load biocontainers
module load survivor

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 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

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