Svtyper

Introduction

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. 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.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/svtyper
Home page: https://github.com/hall-lab/svtyper

Versions

  • 0.7.1

Commands

  • svtyper

  • svtyper-sso

  • python

  • python2

Module

You can load the modules by:

module load biocontainers
module load svtyper

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 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