manta
Link to section 'Introduction' of 'manta' Introduction
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
BioContainers: https://biocontainers.pro/tools/manta
Home page: https://github.com/Illumina/manta
Link to section 'Versions' of 'manta' Versions
- 1.6.0
Link to section 'Commands' of 'manta' Commands
- configManta.py
- python
Link to section 'Module' of 'manta' Module
You can load the modules by:
module load biocontainers
module load manta
Link to section 'Example job' of 'manta' 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 manta on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=manta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers manta
configManta.py --normalBam=HCC1954.NORMAL.30x.compare.COST16011_region.bam \
--tumorBam=G15512.HCC1954.1.COST16011_region.bam \
--referenceFasta=Homo_sapiens_assembly19.COST16011_region.fa \
--region=8:107652000-107655000 \
--region=11:94974000-94989000 \
--exome --runDir="MantaDemoAnalysis"
python MantaDemoAnalysis/runWorkflow.py