bamsurgeon
Link to section 'Introduction' of 'bamsurgeon' Introduction
Bamsurgeon
are tools for adding mutations to .bam files, used for testing mutation callers.
Docker hub: https://hub.docker.com/r/lethalfang/bamsurgeon and its home page on Github.
Link to section 'Versions' of 'bamsurgeon' Versions
- 1.2
Link to section 'Commands' of 'bamsurgeon' Commands
- addindel.py
- addsnv.py
- addsv.py
Link to section 'Module' of 'bamsurgeon' Module
You can load the modules by:
module load biocontainers
module load bamsurgeon
Link to section 'Example job' of 'bamsurgeon' 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 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