What is the BED file format?
The .bed extension identifies Browser Extensible Data, a plain-text tab-delimited format used in computational genomics to describe the coordinates of genomic features. It was developed by the UCSC Genome Bioinformatics Group and is one of the most widely used annotation exchange formats in bioinformatics.
Each row describes one genomic interval. The three mandatory columns are chromosome name (chrom), start position (chromStart), and end position (chromEnd). Up to nine optional columns extend the record with name, score, strand, thick-region boundaries, RGB display color, and exon block structure.
A critical coordinate convention: chromStart is 0-based and chromEnd is 1-based, producing a half-open interval start, end). This differs from [GFF (1-based, closed coordinates) and is a frequent source of off-by-one errors when converting between formats.
Sub-profiles define common usage tiers: BED3 (mandatory columns only), BED6 (adds name, score, strand), and BED12 (adds exon block structure for transcript annotation). Files may include optional track and browser header lines for direct upload to the UCSC Genome Browser or Ensembl. The GA4GH formally standardized the format as BED v1.0 in 2021 after decades of informal use.
For large datasets, the binary indexed bigBed variant (created with bedToBigBed) offers efficient random access. Compressed .bed.gz files are also widely distributed. Common tools include bedtools, IGV, and UCSC Genome Browser.
Security & safety
RISK: LOWPlain text data file; no executable code; safe to open in any text editor or genome browser.
Format details
in a nutshell- InfoSnorkel Blue Elephant Definition file - Niche CRM/contact management software by Blue Elephant Software (Windows); effectively dead/abandoned.
Programs that open BED files
Windows3 apps
Integrated Genome Browser (IGB)
Open-source File → Open Local File, select the .bed file; it loads as a genomic track.
IGV (Integrative Genomics Viewer)
Open-source File → Load from File, select .bed; choose genome assembly matching the file's coordinates. 
macOS2 apps
Linux3 apps
UCSC Genome Browser
Free My Data → Custom Tracks → paste or upload .bed file; select genome assembly. Technical details
deep spec| Encoding | Plain text, tab-delimited (ASCII or UTF-8) |
| Mandatory columns | 3: chrom, chromStart, chromEnd |
| Total defined columns | Up to 12 (3 mandatory + 9 optional per GA4GH BED v1.0) |
| Coordinate system | 0-based start, 1-based end (half-open interval [start, end)) - differs from GFF/GTF 1-based closed intervals |
| Sub-profiles | BED3 (3 cols), BED6 (+ name, score, strand), BED12 (+ exon block structure) |
| Header directives | Optional track and browser lines for UCSC Genome Browser upload; not part of data |
| Compression | None natively; .bed.gz (gzip-compressed) widely distributed |
| Binary indexed variant | bigBed - created with bedToBigBed; supports efficient random access on large datasets |
| Formal specification | GA4GH BED v1.0 (2021); earlier use was informal UCSC convention |
| Strand encoding | + or - character in column 6 (BED6+) |
| RGB color field | itemRgb column (BED9+) - comma-separated R,G,B integer triple for browser display |
| MIME type | text/plain (also text/x-bed) |
| Released | late 1990s, UCSC Genome Browser project; GA4GH BED v1.0 formal spec published 2021 |
| Latest version | GA4GH BED v1.0 (2021) |
| Open standard | Yes · royalty-free |
| Specification | samtools.github.io |
BED conversions
Community Q&A
asked by usersNo questions yet - be the first to ask about BED files.
