RCAC - Software: SVTyper

Software: SVTyper

Type

Resource

Description

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data. svtyper is the original implementation of the genotyping algorithm, and works with multiple samples.

Available Versions

Available Versions
Unspecified:	0.7.1

svtyper-sso is an alternative implementation of svtyper that is optimized for genotyping a single sample. svtyper-sso is a parallelized implementation of svtyper that takes advantage of multiple CPU cores via the multiprocessing module. svtyper-sso can offer a 2x or more speedup (depending on how many CPU cores used) in genotyping a single sample. NOTE: svtyper-sso is not yet stable. There are minor logging differences between the two and svtyper-sso may exit with an error prematurely when processing CRAM files.

BioContainers: https://biocontainers.pro/tools/svtyper
Home page: https://github.com/hall-lab/svtyper

Commands

svtyper
svtyper-sso
python
python2

Module

You can load the modules by:

module load biocontainers
module load svtyper

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 svtyper on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=svtyper
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers svtyper

svtyper \
    -i data/example.vcf \
    -B data/NA12878.target_loci.sorted.bam \
    -l data/NA12878.bam.json \
    > out.vcf