Work

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

Year: 2011

Type: article

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. 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btr032

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

Institutions: National Institutes of Health, St. Jude Children's Research Hospital, National Cancer Institute

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Cancer Institute

Award: G1745638480