Clever-toolkit

Introduction

Clever-toolkit is a collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/clever-toolkit
Home page: https://bitbucket.org/tobiasmarschall/clever-toolkit/src/master/

Versions

  • 2.4

Commands

  • clever

  • laser

  • bam-to-alignment-priors

  • split-priors-by-chromosome

  • clever-core

  • postprocess-predictions

  • evaluate-sv-predictions

  • split-reads

  • laser-core

  • laser-recalibrate

  • genotyper

  • insert-length-histogram

  • add-score-tags-to-bam

  • bam2fastq

  • remove-redundant-variations

  • precompute-distributions

  • extract-bad-reads

  • filter-variations

  • merge-to-vcf

  • multiline-to-xa

  • filter-bam

  • read-group-stats

Module

You can load the modules by:

module load biocontainers
module load clever-toolkit

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 clever-toolkit on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=clever-toolkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers clever-toolkit

cat mapped.bam |  bam2fastq output_1.fq output_2.fq