bamgineer
Link to section 'Introduction' of 'bamgineer' Introduction
Bamgineer is a tool that can be used to introduce user-defined haplotype-phased allele-specific copy number variations (CNV) into an existing Binary Alignment Mapping (BAM) file with demonstrated applicability to simulate somatic cancer CNVs in phased whole-genome sequencing datasets.
Docker hub: https://hub.docker.com/r/suluxan/bamgineer-v2 and its home page on Github.
Link to section 'Versions' of 'bamgineer' Versions
- 1.1
Link to section 'Commands' of 'bamgineer' Commands
- simulate.py
Link to section 'Module' of 'bamgineer' Module
You can load the modules by:
module load biocontainers
module load bamgineer
Link to section 'Example job' of 'bamgineer' 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 Bamgineer on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bamgineer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bamgineer
simulate.py -config inputs/config.cfg \
-splitbamdir splitbams \
-cnv_bed inputs/cnv.bed \
-vcf inputs/normal_het.vcf \
-exons inputs/exons.bed \
-outbam tumour.bam \
-results outputs \
-cancertype LUAC1