BED (Browser Extensible Data) is a text-based file format used to describe genomic regions or features using chromosome coordinates.
Why BED files exist
Many genomics analyses identify locations on the genome rather than producing sequences, such as regulatory regions, genes, or sequencing coverage peaks. BED provides a compact and portable way to store and exchange these genomic intervals.
The format is widely supported by genome browsers and analysis tools.
What a BED file contains
Each line describes one genomic feature using at least three fields: chromosome name, start position, and end position.
Additional optional fields may include feature names, strand direction, display information, or sub-regions such as exon blocks. Files are often described as BED3, BED6, or BED12 depending on how many standard fields are used.
BED coordinates use a 0-based, half-open system, meaning the start position is included while the end position is not. This differs from some other genomic formats and is a common source of confusion.
Where BED appears in pipelines
Typical workflow:
Sequencing → Alignment → Feature detection or annotation → BED file → Visualisation or interpretation
BED files are commonly used to exchange peak calls, gene regions, or analysis targets.
BED and GFF/GTF
BED and GFF/GTF both describe genomic features, but BED is simpler and often used for region lists or browser tracks, while GFF and GTF include richer annotation structure for genes and transcripts.
Relation to Switzerland Omics systems
Switzerland Omics systems operate on variant and feature data that may originate from genomic regions defined in BED files during evidence extraction and interpretation.
Technical specification
The canonical BED format specification is maintained within the hts-specs repository used by GA4GH and samtools:
https://github.com/samtools/hts-specs
