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Biobambam

Introduction ~~~~~~~~ Biobambam is a collection of tools for early stage alignment file processing.

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

Versions

  • 2.0.183

Commands ~~~~~~~ - bam12auxmerge - bam12split - bam12strip - bamadapterclip - bamadapterfind - bamalignfrac - bamauxmerge - bamauxmerge2 - bamauxsort - bamcat - bamchecksort - bamclipXT - bamclipreinsert - bamcollate2 - bamdepth - bamdepthintersect - bamdifference - bamdownsamplerandom - bamexplode - bamexploderef - bamfastcat - bamfastexploderef - bamfastnumextract - bamfastsplit - bamfeaturecount - bamfillquery - bamfilteraux - bamfiltereofblocks - bamfilterflags - bamfilterheader - bamfilterheader2 - bamfilterk - bamfilterlength - bamfiltermc - bamfilternames - bamfilterrefid - bamfilterrg - bamfixmateinformation - bamfixpairinfo - bamflagsplit - bamindex - bamintervalcomment - bamintervalcommenthist - bammapdist - bammarkduplicates - bammarkduplicates2 - bammarkduplicatesopt - bammaskflags - bammdnm - bammerge - bamnumericalindex - bamnumericalindexstats - bamrank - bamranksort - bamrecalculatecigar - bamrecompress - bamrefextract - bamrefinterval - bamreheader - bamreplacechecksums - bamreset - bamscrapcount - bamseqchksum - bamsormadup - bamsort - bamsplit - bamsplitdiv - bamstreamingmarkduplicates - bamtofastq - bamvalidate - bamzztoname

Module

You can load the modules by:

module load biocontainers
module load biobambam

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 Biobambam on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=biobambam
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers biobambam

bammarkduplicates I=Aligned.sortedByCoord.out.bam O=out.bam D=duplcate_out

bamsort I=Aligned.sortedByCoord.out.bam O=sorted.bam sortthreads=8

bamtofastq filename=Aligned.sortedByCoord.out.bam outputdir=fastq_out