Bambino protocols

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Bambino specifications

Information


Unique identifier OMICS_00876
Name Bambino
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michael N. Edmonson <>

Publication for Bambino

Bambino in pipelines

 (7)
2016
PMCID: 5058651
PMID: 27144525
DOI: 10.18632/oncotarget.9093

[…] (hg19) using bwa ([]). pcr duplicated reads are marked and removed using picard (http://picard.sourceforge.net/). putative snvs and indels were identified by running variation detection module of bambino []. a putative mutation was further filtered based on the following criteria: (1) the alternative allele is absent in the paired non-tumor sample; (2) fisher exact test p-value shows […]

2016
PMCID: 5070097
PMID: 27756300
DOI: 10.1186/s12920-016-0226-1

[…] []. pcr duplicated reads were marked and removed by using picard (http://broadinstitute.github.io/picard/). putative snvs and indels were identified by running the variation detection module of bambino []. after initial variant calling, the predicted mutations were further filtered to remove potential false calls: (1) the alternative allele is present in the matched blood sample […]

2016
PMCID: 5363516
PMID: 27823983
DOI: 10.18632/oncotarget.13062

[…] aligned to the ncbi human reference genome (grch37) using bwa []. pcr duplicated reads were marked using picard []. putative snvs and indels were identified by running variation detection module of bambino []. all putative snvs were further filtered based on a standard set of criteria to remove the following common types of false calls: (1) the alternative allele was present in the matching […]

2015
PMCID: 4850888
PMID: 27148567
DOI: 10.1101/mcs.a000380

[…] genome (hg19) using bwa (). pcr duplicated reads were marked using picard (http://picard.sourceforge.net/). putative snvs and indels were identified by running variation detection module of bambino (). after initial variant calling, the predicted mutations were further filtered to remove potential false calls: (1) the alternative alleles were present in both tumor and the matched normal […]

2013
PMCID: 3622303
PMID: 23531725
DOI: 10.1093/gbe/evt031

[…] file using a home-made perl script. the tool indelrealigner in the gatk package () was used to left-align indels so that the same indel would not be represented as a different variant., the bambino program () was used to process the realigned file and detect the indels within it. the following options were set: the minimum number of reads passing all quality filters required […]

Bambino in publications

 (7)
PMCID: 5932012
PMID: 29720585
DOI: 10.1038/s41467-018-04180-1

[…] were created using samtools (1.3.1) and variant calling was performed using varscan (2.4.1). putative mutations were filtered based on quality and resultant variants were manually reviewed using bambino. for calculations of mutant allele frequencies, the number of reads required for the mutant allele was ≥100, otherwise data from the pcr amplicon validation was used. fish plots depicting […]

PMCID: 5712232
PMID: 28825729
DOI: 10.1038/ng.3940

[…] retaining all variants. the first approach applied both atlas and samtools followed by the sacbe annotation pipeline [,]. in the second approach, the bam files were independently analyzed using bambino version 1.05 []. all non-silent variants from both wgs and wes were combined into a single file and annotated with the oncotator program (http://www.broadinstitute.org/oncotator/). missense […]

PMCID: 5058651
PMID: 27144525
DOI: 10.18632/oncotarget.9093

[…] (hg19) using bwa ([]). pcr duplicated reads are marked and removed using picard (http://picard.sourceforge.net/). putative snvs and indels were identified by running variation detection module of bambino []. a putative mutation was further filtered based on the following criteria: (1) the alternative allele is absent in the paired non-tumor sample; (2) fisher exact test p-value shows […]

PMCID: 4850888
PMID: 27148567
DOI: 10.1101/mcs.a000380

[…] by a realignment process to filter out false calls introduced by germline events, mapping artifacts, and homopolymer. prior to validation, the predicted mutations were manually inspected using bambino viewer () to remove false calls introduced by mapping or alignment artifacts. the putative mutations passing manual review were segregated into high and low confidence groups according […]

PMCID: 3739863
PMID: 23708854
DOI: 10.1007/s10522-013-9433-8

[…] million reads, ~50 % of reads generated were mapped). all data have been submitted to geo under the accession gse34272 (wood et al. ). a mismatch analysis was performed on the aligned reads using bambino in order to generate candidate editing sites (edmonson et al. ). these candidates were selected using custom python scripts for a-g mismatches within exons in genes on the positive strand, […]

Bambino institution(s)
Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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