title: Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.
abstract: CONCLUSIONS
  Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs.
  
  
  BACKGROUND
  Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally.
authors.affiliation: National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. edmonson@nih.gov
authors.forename: Michael N
authors.initials: MN
authors.lastname: Edmonson
authors.forename: Jinghui
authors.initials: J
authors.lastname: Zhang
authors.forename: Chunhua
authors.initials: C
authors.lastname: Yan
authors.forename: Richard P
authors.initials: RP
authors.lastname: Finney
authors.forename: Daoud M
authors.initials: DM
authors.lastname: Meerzaman
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Buetow
mesh_terms: D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D004252:DNA Mutational Analysis / Q000379:methods*; D005787:Gene Frequency; D023281:Genomics / Q000379:methods; D005838:Genotype; D020407:Internet; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment / Q000379:methods*; D012984:Software