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