Bam-readcount

Introduction

Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.

For more information, please check its | Docker hub: https://hub.docker.com/r/mgibio/bam-readcount and its home page on Github.

Versions

• 1.0.0

Commands

• bam-readcount

Module

You can load the modules by:

module load biocontainers
module load bam-readcount

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 Bam-readcount on our clusters:

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

module --force purge
ml biocontainers bam-readcount

bam-readcount -f Homo_sapiens.GRCh38.dna.primary_assembly.fa Aligned.sortedByCoord.out.bam