biobambam protocols

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biobambam specifications


Unique identifier OMICS_04664
Name biobambam
Alternative name biobambam2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS
Programming languages C++, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.87
Stability Stable
Maintained Yes


  • bamcollate2
  • bammarkduplicates
  • bammaskflags
  • bamrecompress
  • bamsormadup
  • bamsort
  • bamtofastq



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  • person_outline German Tischler <>

Publication for biobambam

biobambam in pipelines

PMCID: 5522380
PMID: 28531267
DOI: 10.1093/gigascience/gix038

[…] 4.1% for the low-coverage and 11.9% versus 13.1% for wes. this difference is likely due to a combination of the improved assembly and a different software package for marking pcr duplications (biobambam here and gatk for grch37). the coverage statistics noted above and presented in table  were calculated using the gatk calculatehsmetrics function and are very similar for both grch37 […]

PMCID: 5615344
PMID: 28837078
DOI: 10.3390/genes8090210

[…] sequence reads were aligned using burrows-wheeler aligner (bwa) [] against human genome 19 (hg19) with decoy sequences [] with the default parameters, then duplicate reads were marked using biobambam2 []. the aligned reads were sorted by the genomic coordinate using sambamba processor [] and stored in bam format files. single nucleotide polymorphism (snps), short insertion-deletion […]

PMCID: 5703905
PMID: 29180744
DOI: 10.1038/s41467-017-01992-5

[…] platform at the wellcome trust sanger institute at 30× depth. raw pair end sequencing reads were aligned with bwa-mem to the grcm38 mouse reference genome. duplicated reads were marked using biobambam. somatic variants were detected using caveman, an expectation maximisation-based somatic substitution-detection algorithm. detected somatic variants were then filtered using an array […]

PMCID: 4910022
PMID: 27291893
DOI: 10.1038/ncomms11845

[…] (build 37, version hs37d5), using bwa mem (version 0.7.8 with minimum base quality threshold set to zero [-t 0] and remaining settings left at default values), followed by coordinate sorting with bamsort (with compression option set to fast (1)) and marking duplicate read pairs with bammarkduplicates (with compression option set to best (9); both part of biobambam package version 0.0.148)., […]

PMCID: 5147911
PMID: 27936026
DOI: 10.1371/journal.pone.0167600

[…] and contained no secondary alignments. these high quality miseq fastq files were then assembled with the previously phased minion reads, which were also converted into fastq files with bedtools bamtofastq []. the hybrid assembly (using both minion and miseq data) was performed on each individual using spades [] with 10 iterations of bayes hammer read correction (-i 10) and aligned with bwa […]

biobambam in publications

PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] (build 37, version hs37d5), using bwa mem (version 0.7.8 with minimum base quality threshold set to zero [−t 0] and remaining settings left at default values), followed by coordinate-sorting with bamsort (with compression option set to fast (1)) and marking duplicate read pairs with bammarkduplicates (with compression option set to best (9)) (both part of the biobambam package version […]

PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] of response to immunotherapy in melanoma patients []. reads were aligned against the grch37d5 reference genome using the sanger cgpmap workflow []. this workflow uses bwa-mem (v0.7.15–1140) [] and biobambam2 (v2.0.69) [] to generate genome coordinate-sorted alignments with duplicates marked. realignment around indels and base recalibration were performed using genome analysis toolkit (v3.6) […]

PMCID: 5861150
PMID: 29593723
DOI: 10.3389/fimmu.2018.00462

[…] to be converted to fasta or fastq format either by running scripts that are part of the software platform (sffinfo-roche; bcl2fastq-illumina) or by using one of the many freely available scripts (bamtofastq, sff_extract). fasta and fastq are the two common input formats for most analysis programs. fasta format consists of a list of sequences with a unique identification tag preceding […]

PMCID: 5829973
PMID: 29503865
DOI: 10.1126/sciadv.aao0665

[…] (gatk) best practices pipeline for variant discovery. namely, the bam file was further prepared with the tools cleansam and addorreplacereadgroups in picard, and read duplicates were marked with biobambam. reads were realigned using the tool realignertargetcreator from gatk, where both the dbsnp variant database and the individual-/strain-specific variant sites were used for the “-known” […]

PMCID: 5723261
PMID: 29234696
DOI: 10.1016/j.dib.2017.11.049

[…] technologies). the isps were loaded and sequenced on a 318 chip (life technologies)., raw sequence reads were obtained from the ion torrent server in bam format and converted to fastq using the bamtofastq program from the bedtools package . reads with more than 20% of the bases with phred score (q) smaller than 20 where removed using the fastq_quality_filter script from the fastx-toolkit […]

biobambam institution(s)
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
biobambam funding source(s)
Supported by the Wellcome Trust.

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