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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Michael N. Edmonson

Publication for Bambino

Bambino citations

 (13)
library_books

De novo activating mutations drive clonal evolution and enhance clonal fitness in KMT2A rearranged leukemia

2018
Nat Commun
PMCID: 5932012
PMID: 29720585
DOI: 10.1038/s41467-018-04180-1

[…] iles 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 clon […]

library_books

A Children's Oncology Group and TARGET Initiative Exploring the Genetic Landscape of Wilms Tumor

2017
Nat Genet
PMCID: 5712232
PMID: 28825729
DOI: 10.1038/ng.3940

[…] ined, 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 va […]

library_books

Exome sequencing analysis of murine medulloblastoma models identifies WDR11 as a potential tumor suppressor in Group 3 tumors

2017
Oncotarget
PMCID: 5630286
PMID: 29029386
DOI: 10.18632/oncotarget.19642

[…] mouse strains. The entire process of single nucleotide variations (SNVs) identification, filtering and validation is illustrated in Figure . Specifically, the initial SNV calling was performed using Bambino [] by comparing each tumor with publicly available normal sequences of C57BL/6 mouse strain []. With filtering and manual curation, 213 putative mutations remained. Amplicon sequencing by Sang […]

library_books

Collecting duct carcinoma of the kidney is associated with CDKN2A deletion and SLC family gene up regulation

2016
Oncotarget
PMCID: 5058651
PMID: 27144525
DOI: 10.18632/oncotarget.9093

[…] ome (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 that numb […]

library_books

MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours

2015
Nat Commun
PMCID: 4686660
PMID: 26635203
DOI: 10.1038/ncomms10013

[…] lumina HiSeq platform. Variant calling from the aligned BAM files was performed using both ATLAS and SAMtools and annotation and filtering was performed using the SACBE annotation pipeline as well as Bambino Version 1.05 (ref. ). Pipelines for both WGS and WES identified single missense, insertion and deletion variants in exons. […]

call_split

Germline Genetic Variation in ETV6 and Risk of Childhood Acute Lymphoblastic Leukemia: a Systematic Genetic Study

2015
PMCID: 4684709
PMID: 26522332
DOI: 10.1016/S1470-2045(15)00369-1
call_split See protocol

[…] a HiSeq 2500 platform with a coverage of 10× for > 84% ∼ 94% of target regions. Sequencing reads were mapped using the Burrow-Wheller Aligner and variant calls in the gene coding regions were made by bambino (with parameters: -min-quality 20, -min-flanking-quality 20, -min-alt-allele-count 3, -min-minor-frequency 0, -broad-min-quality 10, -mmf-max-hq-mismatches 4, -mmf-max-hq-mismatches-xt-u 10, - […]

Citations

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

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