All about CRAM Files

The CRAM file type is primarily associated with samtools.

CRAM	File extension: CRAM
	File type:	compressed file format

What is a CRAM file?

CRAM files mostly belong to samtools. CRAM files come in two main forms:
Genomic data: These files are compressed BAM files that store sequence alignment records using reference‐based compression. They reduce storage needs for large genomic data sets. Use specialized tools like samtools to view and convert them. More details are available at HTSlib.
ROM file systems: A smaller group of CRAM files are compressed ROM File System files used to keep a compact image of a file system in embedded devices.
Key details provided by FilExt.com:

Data type: Stores genomic sequence data or ROM file system images.

Function: Uses compression techniques to reduce file size while maintaining data integrity.

Usage: Applied in bioinformatics for sequence alignment and in embedded systems for ROMFS images.

FilExt.com note: These files require specific software to extract and inspect their contents.

How to open a CRAM file

You need a suitable software like samtools to open a CRAM file. Without proper software you will receive a Windows message "How do you want to open this file?" or "Windows cannot open this file" or a similar Mac/iPhone/Android alert. If you cannot open your CRAM file correctly, try to right-click or long-press the file. Then click "Open with" and choose an application. You can also display a CRAM file directly in the browser:. Just drag the file onto this browser window and drop it.

Online CRAM Text Viewer

Choose your .cram file to analyze

or drag and drop it here

Online File Viewer

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Programs that open and convert CRAM files:

samtools
See the previous paragraphs to learn more about the main application. CRAM files are often referred to as samtools compresseds because this type of file is primarily created or used by this software.
Compressed ROM File System
In UNIX/Linux variants you use mkcramfs to create a .CRAM file which is a compressed ROM file system image from the contents of a given directory. Cram file systems are used for Debian INITRD images.

CRAM file format:

A file format defines how the data in the file is structured. The first characters in a file identify the file format, for example, HTML files start with the bytes <html>. If the file extension or signature does not match the file format, errors will occur when opening or editing the file. Knowledge is power - this also applies when dealing with unknown or faulty files. Below you will find our evaluation of the CRAM files:

CRAM is rarely used as a file extension and predominantly uses a uniform format. The file formats most commonly found in CRAM files are:

80% of all CRAM files belong to Compressed Alignment format. The contents of these files cannot be read by a human; only a computer program can interpret the data. The files are often between 13 MB and 7 GB in size. The file type is relatively new. The keywords CRAM are typical for these files. Files like these are about sortdup, bqsr, bwamem, grch, sorted, recal, exome and noalt.
15% of all CRAM files start with the bytes E=Í( crucial for this file format. If you open these files in a text editor, you will see only illegible characters. The files are often between 1 MB and 49 MB in size. The files contain the following words: Compressed, Compressed ROMFS and init.plug-in.sh. Such files sometimes refer to seat, images, poster and meta.

All other CRAM files (5%) have no uniform format. These files sometimes refer to coverage or sample. You can get all the details of your CRAM file by dragging it onto this page or by clicking the button "Choose your .cram file to analyze" above.

Technical Data for CRAM File Extension

File classification:

Compressed

Related files:

bam, sam, fastq, fasta, cramfs, crai, md5, gz, loop, zip, vcs, inkml, magnet, img

a cram compressed file format is a special file format and should only be edited and saved with the appropriate software.

How to solve problems with CRAM files

Associate the CRAM file extension with the correct application.
Update your software that should actually open compressed file formats. Because only the current version supports the latest CRAM file format. Search, therefore, e.g. on the manufacturer website after an available samtools update.
To make sure that your CRAM file is not corrupted or virus-infected, get the file again and scan it with Google's virustotal.com.
Click here to open your .CRAM file online - secure, fast, and no downloads needed.