biobambam pipeline

biobambam specifications

Information


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
Requirements libmaus2
Maintained Yes

Subtools


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

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Versioning


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Documentation


Maintainer


  • person_outline German Tischler <>

Publication for biobambam

biobambam IN pipelines

 (5)
2017
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 tableĀ 1 were calculated using the gatk calculatehsmetrics function and are very similar for both grch37 […]

2016
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)., […]

2016
PMCID: 4910022
PMID: 27291893
DOI: 10.1038/ncomms11845

[…] 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)., the generated bam files were used to identify snvs by applying samtools mpileup33 […]

2016
PMCID: 4910022
PMID: 27291893
DOI: 10.1038/ncomms11845

[…] 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)., the generated bam files were used to identify snvs by applying samtools mpileup33 (version 0.1.19 with parameter settings -rei -q 30 -ug) with output piped […]

2016
PMCID: 5224498
PMID: 27614072
DOI: 10.1093/nar/gkw805

[…] (http://www.1000genomes.org/home) and the shmirhcv318 as separate contig using the bwa-mem (v0.7.8) software (39). resulting bam files were coordinate-sorted, merged and pcr duplicates marked by biobambam (v0.0.148) software (40). the resulting bam files have an average coverage of 19.82x and 21.69x for wt and t2 31.3 cells, respectively (0x and 12.69x on the shmirhcv318 contig). […]

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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