Bambino: A variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

Michael N. Edmonson, Jinghui Zhang, Chunhua Yan, Richard P. Finney, Daoud M. Meerzaman, Kenneth H. Buetow

Research output: Contribution to journalArticle

59 Scopus citations

Abstract

Summary: 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 nonreference allele frequencies, and predict protein-coding changes caused by SNPs. Published by Oxford University Press on behalf of the US Government 2011.

Original languageEnglish (US)
Article numberbtr032
Pages (from-to)865-866
Number of pages2
JournalBioinformatics
Volume27
Issue number6
DOIs
StatePublished - Mar 1 2011
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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