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

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 biomedical 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 https://github.com/CBMi-BiC/bamchop.