BAMDateien

BAMDateien are binary files that store genomic sequence alignment data. They are used in bioinformatics to efficiently represent the output of read mapping tools that align short DNA reads to a reference genome. The file format is part of the SAM (Sequence Alignment/Map) family, which also includes the human‑readable SAM text format. A BAM file provides a compressed representation of the SAM data, enabling faster access and reduced storage requirements.

A typical BAM file includes a header section followed by a series of alignment records. The header contains metadata such as the reference sequence dictionary, program information, and read group details. Each alignment record stores the read name, mapping position, quality metrics, clipping information, and optional tags that convey additional information like mapping quality or alignment flags. The binary encoding of the data allows for quick compression of repetitive fields and efficient random access when paired with an index file.

BAM files are widely used in downstream genomic analyses, including variant calling, coverage calculation, and transcriptome quantification. They are often accompanied by a BAI index, which allows tools to retrieve alignments overlapping a specific genomic interval without scanning the entire file. Common software for creating, viewing, and manipulating BAM files includes samtools, bowtie, bwa, and IGV. Proper handling of BAM files is essential for reproducibility in high‑throughput sequencing projects and for maintaining data integrity during analysis pipelines.