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

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.