biobambam
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'biobambam' Versions
- 2.0.183
Link to section 'Commands' of 'biobambam' 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
Link to section 'Module' of 'biobambam' Module
You can load the modules by:
module load biocontainers
module load biobambam
Link to section 'Example job' of 'biobambam' Example job
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