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Bamchop: A bioinformatics utility to summarize and visualize exome and other types of targeted resequencing data

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8 Author(s)
Zhe Zhang ; Center for Biomed. Inf., Children''s Hosp. of Philadelphia, Philadelphia, PA, USA ; Leipzig, J. ; Sasson, A. ; Perin, J.C.
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Targeted resequencing projects can generate massive amount of data in the form of short nucleic acid sequences. These sequences are aligned to a reference genome and stored in BAM (Binary Alignment/Map) files in most cases. A growing challenge for biomédical researchers is to rapidly summarize large BAM files (typically 5 to 25 GB) to evaluate data quality and guide follow-up steps. Here, we present an R package and report template, "bamchop", that retrieves targeted resequencing information from a BAM file and illustrates it in a standardized format. This program is applicable to all resequencing data that investigates selected genomie regions, ranging from a small number of mutation hotspots to a complete human exome. Bamchop reports the sequencing quality and coverage, mapping confidence, strand and nucleic acid bias, and other information about the targeted regions and genomie background. A bamchop report is the product of Sweave framework that requires the LaTeX document preparation system and the R statistical environment. In applying it to a variety of resequencing projects, we determined that bamchop is a powerful tool for both bioinformaticians and bench scientists to conveniently assess their resequencing data. The source code of bamchop is available from

Published in:

Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on

Date of Conference:

4-7 Oct. 2012