Manta

Introduction

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/manta
Home page: https://github.com/Illumina/manta

Versions

1.6.0

Commands

configManta.py
python

Module

You can load the modules by:

module load biocontainers
module load manta

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 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