CRAM is a more highly compressed alternative to the BAM and SAM DNA sequence alignment file formats.

CRAM is a format designed by the European Bioinformatics Institute. It uses reference based compression, meaning that only base calls that differ to a designated reference sequence need to be stored. 

See for the EBI’s documentation. Typically CRAM achieves 40-50% space saving over the alternative BAM format. The CRAM specification can be found at the page along with related formats.


Packages supporting the CRAM format include Samtools/Htslib, Scramble, Cramtools and Picard/Htsjdk. Please download one of those to get support for the file format.


If you need help or have any queries, please contact us using the details below.

A generic email list is shared for all associated alignment formats at or use the tool specific github pages for submitting issues.

Sanger Institute Contributors

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James Bonfield

Principal Software Developer

External Contributors

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Vadim Zalunin


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