clever-toolkit
Link to section 'Introduction' of '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.
BioContainers: https://biocontainers.pro/tools/clever-toolkit
Home page: https://bitbucket.org/tobiasmarschall/clever-toolkit/src/master/
Link to section 'Versions' of 'clever-toolkit' Versions
- 2.4
Link to section 'Commands' of 'clever-toolkit' 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
Link to section 'Module' of 'clever-toolkit' Module
You can load the modules by:
module load biocontainers
module load clever-toolkit
Link to section 'Example job' of 'clever-toolkit' 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 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