Preparbam

Preparbam is a software tool designed to preprocess BAM files produced in high-throughput sequencing workflows. It focuses on preparing data for downstream analyses such as variant calling by applying a suite of quality control, formatting, and normalization steps. The goal is to produce consistent, analysis-ready data while preserving important alignment information.

Key features include validation of BAM integrity, sorting by genomic coordinate, indexing, and conversion between formats. It provides read-level filtering by mapping quality and flag-based criteria, and offers options for removing or marking duplicate reads. Preparbam can harmonize headers and read groups across multiple input files and supports merging or splitting datasets. The tool is designed to operate in multi-threaded environments and can stream data from standard input and to standard output to fit into existing pipelines.

Usage and compatibility: Preparbam accepts BAM, SAM, or CRAM inputs and outputs cleaned BAM files suitable for downstream analysis. It is designed to interoperate with established workflows and tools in genomics pipelines and can be used alongside popular variant callers and benchmarking workflows. Optional output of quality control metrics and logs helps summarize the modifications performed.

Implementation and availability: Preparbam is an open-source project implemented as a modular command-line tool and library. It emphasizes compatibility with common HTS data access libraries, enabling support for standard file formats across major operating systems. Documentation typically covers installation, command-line options, and example workflows.

Impact and considerations: As with any preprocessing step, users should tailor the workflow to their analysis goals, since different applications impose varying requirements for reads and duplicates. Validation of preprocessing outcomes and careful review of any changes to read groups or headers are advised before downstream analyses.