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

M. N. Edmonson, J. Zhang, C. Yan, R. P. Finney, D. M. Meerzaman, K. H. Buetow
2011 Bioinformatics  
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
more » ... es from a UCSC genome annotation database, display histograms of nonreference 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.
doi:10.1093/bioinformatics/btr032 pmid:21278191 pmcid:PMC3051333 fatcat:ygsmvpac3bevvdzztxzn53gu3m