svaba
Link to section 'Introduction' of 'svaba' Introduction
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.
BioContainers: https://biocontainers.pro/tools/svaba
Home page: https://github.com/walaj/svaba
Link to section 'Versions' of 'svaba' Versions
- 1.1.0
Link to section 'Commands' of 'svaba' Commands
- svaba
Link to section 'Module' of 'svaba' Module
You can load the modules by:
module load biocontainers
module load svaba
Link to section 'Example job' of 'svaba' 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 svaba on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=svaba
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers svaba
DBSNP=dbsnp_indel.vcf
TUM_BAM=G15512.HCC1954.1.COST16011_region.bam
NORM_BAM=HCC1954.NORMAL.30x.compare.COST16011_region.bam
CORES=8 ## set any number of cores
REF=Homo_sapiens_assembly19.COST16011_region.fa
svaba run -t $TUM_BAM -n $NORM_BAM \
-p $CORES -D $DBSNP \
-a somatic_run -G $REF