Bamutil

Introduction

Bamutil is a collection of programs for working on SAM/BAM files.

For more information, please check its website: https://biocontainers.pro/tools/bamutil and its home page on Github.

Versions

• 1.0.15

Commands

• bam

Module

You can load the modules by:

module load biocontainers
module load bamutil

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 Bamutil on our clusters:

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

module --force purge
ml biocontainers bamutil

bam validate --params --in test/testFiles/testInvalid.sam --refFile test/testFilesLibBam/chr1_partial.fa --v --noph 2> results/validateInvalid.txt

bam convert --params --in test/testFiles/testFilter.bam --out results/convertBam.sam --noph 2> results/convertBam.log

bam  splitChromosome --in test/testFile/sortedBam1.bam --out results/splitSortedBam --noph 2> results/splitChromosome.txt

bam stats --basic --in test/testFiles/testFilter.sam --noph 2> results/basicStats.txt

bam gapInfo --in test/testFiles/testGapInfo.sam --out results/gapInfo.txt --noph 2> results/gapInfo.log

bam findCigars --in test/testFiles/testRevert.sam --out results/cigarNonM.sam --nonM --noph 2> results/cigarNonM.log