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.BED file extension

To open .BED files on Windows, if the file is a genomic BED file, open it first in a plain-text editor to confirm it contains rows of chromosome or sequence names and coordinate columns.

To open a .BED file, first determine whether it is a genomic BED text file or a binary .BED file from another application. Genomic BED files can be viewed in a text editor and opened in tools such as IGV Desktop, UCSC Genome Browser, or bedtools; PLINK .bed files should be opened with PLINK together with their matching .bim and .fam files.

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Last updated: April 29, 2026 · Reviewed by Julian Stricker

Open on your device

Choose your operating system for a dedicated step-by-step opening guide.

How to open .BED files

Use these platform-specific instructions to open .BED files safely.

Windows

  1. If the file is a genomic BED file, open it first in a plain-text editor to confirm it contains rows of chromosome or sequence names and coordinate columns.
  2. For visual inspection, open the file in IGV Desktop or load it as a custom track in the UCSC Genome Browser.
  3. For command-line analysis, use a compatible bioinformatics workflow such as bedtools where available.
  4. If the .bed file came with matching .bim and .fam files, treat it as a PLINK binary genotype file and open it with PLINK instead of a genome browser.
Full Windows guide

Mac

  1. Control-click the file and choose Open With, then use a plain-text editor to check whether it is a text-based genomic BED file.
  2. Open genomic BED annotation tracks in IGV Desktop or load them into the UCSC Genome Browser.
  3. If the file is part of a PLINK dataset, keep the .bed, .bim, and .fam files together and use PLINK.
  4. If the file is binary and you do not know its source, ask the sender or the generating application which .BED format it uses.
Full Mac guide

Linux

  1. Use a text viewer such as less, head, or a plain-text editor to check whether the file is a whitespace-delimited genomic BED file.
  2. Use bedtools for command-line operations on BED3, BED4, BED5, BED6, or BED12-style files.
  3. Use IGV Desktop or the UCSC Genome Browser for visualizing genomic annotation tracks.
  4. If the file belongs to a PLINK dataset, use PLINK with the associated .bim and .fam files.
Full Linux guide

iOS

  1. iOS has no typical native support for bioinformatics BED workflows; if the file is small and text-based, preview it in Files or a text editor only to inspect its contents.
  2. For real analysis or visualization, transfer the file to a desktop system or use a supported web workflow such as the UCSC Genome Browser.
Full iOS guide

Android

  1. Android has no typical native support for BED analysis; if the file is text-based, use a trusted text viewer only for quick inspection.
  2. For visualization or processing, move the file to a desktop environment with IGV Desktop, bedtools, PLINK, or a browser-based genome tool as appropriate.
Full Android guide

Security notes

  • Genomic BED files are normally plain text and do not contain macros, but malformed or extremely large files can still crash or slow down parsers and viewers.
  • BED files may contain sensitive genomic coordinates or sample-related annotations; treat shared files as potentially private research or health-related data.
  • Do not assume every .BED file is safe text: PLINK .bed and the registered RealVNC .bed media type are binary formats and should be opened only with the intended software.
  • Be cautious when loading untrusted BED files into web services, because uploading the file may disclose its contents to that service.

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Can't open this file?

These are the most common causes and fixes when .BED files fail to open.

Common reasons

  • The .BED file opens as unreadable binary data
  • A genome browser or IGV does not load the file
  • bedtools gives unexpected results
  • The file is too large to open on a phone or in a basic editor

Fix steps

  1. Check whether the file came with .bim and .fam files; if so, open it with PLINK.
  2. Check the file source or ask the sender which application created it.
  3. Do not convert a binary .BED file by saving it from a text editor, because this can corrupt it.

OS-specific troubleshooting

What is a .BED file?

In genomics, BED means Browser Extensible Data: a whitespace-delimited feature format for describing intervals on reference sequences. Standard BED has three required fields and up to nine additional fields, commonly referred to as BED3 through BED12. The .bed extension is ambiguous: IANA registers application/vnd.realvnc.bed for a binary RealVNC vendor format, and PLINK uses .bed for a separate binary genotype table that is not the same as UCSC/HTS BED.

Background

The most common practical use of .bed files is in bioinformatics. A genomic BED file stores genomic intervals such as genes, variants, peaks, or annotation tracks, typically using columns for chromosome or sequence name, start coordinate, and end coordinate, with optional columns for names, scores, strand, and richer feature information.

Common MIME types: application/vnd.realvnc.bed

Further reading

Authoritative resources for more details on the .BED format.

Common .BED issues

The .BED file opens as unreadable binary data

Not every .BED file is a text-based genomic BED file. PLINK .bed files are binary genotype tables, and IANA also registers .bed for a binary RealVNC vendor data format.

  1. Check whether the file came with .bim and .fam files; if so, open it with PLINK.
  2. Check the file source or ask the sender which application created it.
  3. Do not convert a binary .BED file by saving it from a text editor, because this can corrupt it.

A genome browser or IGV does not load the file

Genomic BED files must follow the expected column structure and must match the genome or reference assembly being viewed.

  1. Confirm the file has at least the three required BED fields.
  2. Check that columns are separated by whitespace or tabs and that there are no broken or inconsistent rows.
  3. Make sure chromosome or sequence names match the reference genome used in the viewer.

bedtools gives unexpected results

Unexpected output often comes from using the wrong .BED variant, inconsistent fields, or data that does not follow the BED specification expected by the tool.

  1. Confirm the file is a genomic BED text file, not a PLINK or RealVNC binary file.
  2. Check whether your data is BED3, BED4, BED5, BED6, or BED12 and use options appropriate for that structure.
  3. Validate a few lines manually against the BED format documentation before running large analyses.

The file is too large to open on a phone or in a basic editor

Genomic BED files can be very large annotation or interval datasets, and mobile apps or simple editors may freeze or truncate the file.

  1. Use desktop bioinformatics tools or a genome browser instead of a mobile viewer.
  2. Inspect only the first few lines with command-line tools before loading the entire file.
  3. If you only need a subset, filter or split the data with an appropriate desktop workflow.

FAQ

What program opens a .BED file?

For genomic BED files, use IGV Desktop, UCSC Genome Browser, bedtools, or a plain-text editor for inspection. For PLINK .bed files, use PLINK with the matching .bim and .fam files. If the file is a RealVNC vendor .BED file, use the application or workflow that created it.

Is a .BED file a text file?

A standard genomic Browser Extensible Data file is a whitespace-delimited text file. However, the same .bed extension is also used for binary formats, notably PLINK genotype data and the RealVNC media type registered with IANA.

Can I rename another file to .bed to convert it?

No. Renaming changes only the file extension. To create a valid genomic BED file, export or convert the data so it follows the BED column rules; for PLINK or RealVNC binary data, use the appropriate application workflow.

Why does my .BED file need .BIM and .FAM files?

That indicates it is likely a PLINK binary genotype dataset. In PLINK, the .bed file stores genotype data and is used together with companion .bim and .fam files; it is not the same as UCSC genomic BED annotation text.

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