Windows
Compatible applications
Quick Facts
Basic information about this file format
Extension
.CRAM
File Type
CRAM (Compressed Reference-oriented Alignment Map)
Category
Data
Best first step
Use compatible software
Quick Summary
A practical overview of the .cram file format
The CRAM file format is a highly efficient, compressed data format used primarily in the field of bioinformatics and genomics for storing biological sequences aligned to a reference genome. Developed by the European Bioinformatics Institute (EBI) and maintained as a standard by the Global Alliance…
File extension
.CRAM
File type
CRAM (Compressed Reference-oriented Alignment Map)
Category
Data
Recommended action
Open with a trusted compatible app
How to open a .cram file
Start with a trusted app that supports this format
- Check the file extension carefully and confirm that the file name really ends with .cram.
- Use software that supports this file type. If one app does not work, try another compatible program for the same platform.
- Update the application if the file was created by a newer version of the software.
- Scan files from unknown sources before opening them, especially documents, archives, scripts, installers, and executable files.
What is a .cram file?
File extension details and usage information
The CRAM file format is a highly efficient, compressed data format used primarily in the field of bioinformatics and genomics for storing biological sequences aligned to a reference genome. Developed by the European Bioinformatics Institute (EBI) and maintained as a standard by the Global Alliance for Genomics and Health (GA4GH), CRAM was designed as a more compact successor to the BAM (Binary Alignment Map) format. The primary innovation of CRAM is its use of reference-based compression; instead of storing every nucleotide in a sequence read, it only records the differences between the read and a specific reference sequence. This approach, combined with advanced entropy coding techniques, allows CRAM files to be significantly smaller than their BAM counterparts, often achieving a 30-60% reduction in storage requirements. This is crucial for large-scale sequencing projects where data storage costs are a major concern. CRAM supports both lossless compression, which preserves all original data including quality scores, and lossy compression modes that can further reduce size by binning quality scores. It also supports random access through the use of companion index files, typically ending in the .crai extension, making it suitable for high-performance computing environments and cloud-based genomic analysis.
Software Compatibility
Programs that may open or work with .cram files
macOS
Compatible applications
Linux
Compatible applications
Mobile
Mobile applications
Can .cram files be converted?
Options for saving or exporting this file to another format
In many cases, a .cram file can be converted by opening it in compatible software and using an option such as Save As, Export, or Convert. The available output formats depend on the file type and the application used.
- Use the original software that created the file when possible.
- Check whether the application supports exporting to common formats.
- Be careful with online converters when working with private, business, or sensitive files.
- If conversion fails, the file may be corrupted, incomplete, encrypted, or not actually a .cram file.
Why can't I open a .cram file?
Common reasons this file type may not open correctly
Wrong software
The file may require a specific program that supports the .cram format.
Incorrect extension
The file extension may have been renamed manually, even though the actual file format is different.
Corrupted file
The file may be incomplete, damaged during download, or transferred incorrectly.
Outdated app
Your software may need to be updated before it can open newer versions of this file format.
Frequently Asked Questions
Common questions about .cram files
To open a .cram file, use software that supports this file format.
- IGV (Integrative Genomics Viewer)
- SAMtools (via WSL)
- HTSlib
- SAMtools
- Bamview
Open the file in compatible software and look for options such as Save As, Export, or Convert. If no export option is available, the file may require a specialized converter or the original application that created it.
- Verify that the file extension is correct.
- Install or update compatible software.
- Try another application that supports this format.
- Check whether the file is corrupted, incomplete, or encrypted.
A file extension alone does not guarantee whether a file is safe or unsafe. Only open files from trusted sources, scan unknown files before opening them, and be especially careful with executable, script, archive, and document files.
File safety tips
Use caution with unknown files
Only open files from trusted sources. Before opening a .cram file, scan it with antivirus software, verify that the file extension is expected, and avoid running unknown executable, installer, macro-enabled document, or script files.