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