Bamsurgeon

Introduction

Bamsurgeon are tools for adding mutations to .bam files, used for testing mutation callers.

For more information, please check its | Docker hub: https://hub.docker.com/r/lethalfang/bamsurgeon and its home page on Github.

Versions

  • 1.2

Commands

  • addindel.py

  • addsnv.py

  • addsv.py

Module

You can load the modules by:

module load biocontainers
module load bamsurgeon

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 Bamsurgeon on our clusters:

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

module --force purge
ml biocontainers bamsurgeon

addsv.py -p 1 -v test_sv.txt -f testregion_realign.bam \
    -r reference.fasta -o testregion_sv_mut.bam \
    --aligner mem --keepsecondary --seed 1234 \
    --inslib test_inslib.fa