Svaba

Introduction

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/svaba

Home page: https://github.com/walaj/svaba

Versions

• 1.1.0

Commands

• svaba

Module

You can load the modules by:

module load biocontainers
module load svaba

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 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