Pubmed Link

Bioinformatics. 2011 Jan 28. [Epub ahead of print]

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

Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman D, Buetow KH.

Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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 a 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.
AVAILABILITY: 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.
CONTACT: edmonson@nih.gov.