confirmbam

ConfirmBam is a software utility designed to validate and verify Binary Alignment Map (BAM) files produced in next-generation sequencing workflows. It focuses on assessing adherence to the SAM/BAM specification, detecting corruption or truncation, and ensuring consistency with associated index files and reference sequences. The goal is to identify errors early in data processing where downstream analyses may be affected.

Core features include format and header validation; record-level checks for flags, read groups, and pairing information; verification of reference sequence identifiers and contig lengths; and consistency checks between BAM records and the index (.bai/.csi). It can also verify alignment coordinates, mate positions, and mapping qualities, and report anomalies. It generates a concise human-readable report and can emit machine-readable output (e.g., JSON) for pipeline integration.

Usage typically involves running the command-line tool with an input BAM, a reference genome when required, and an output report path. Examples: confirmbam sample.bam --reference ref.fa --output report.json. It is designed to work with streaming input and to be compatible with common HTS tooling, such as SAMtools and bcftools workflows, without modifying the original data.

Implementation notes: ConfirmBam is designed to be fast and memory-efficient on large BAM files, leveraging the HTSlib ecosystem and parallel processing where available. It supports common compression formats and generally operates under permissive open-source licenses. Limitations include that it only validates integrity and conformity; it does not correct errors in the data.

See also: BAM format, SAM format, HTSlib, Picard, SAMtools.