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 datsets.

For more information, please check its | Docker hub: https://hub.docker.com/r/suluxan/bamgineer-v2 and its home page on Github.

Versions

1.1

Commands

simulate.py

Module

You can load the modules by:

module load biocontainers
module load bamgineer

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 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