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

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

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 non-reference allele frequencies, and predict protein-coding changes caused by SNPs

Topics: Applications Note
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3051333
Provided by: PubMed Central
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