Scramble can convert between SAM, BAM and CRAM file formats.  It is a part of the Staden io_lib package.

In this regard it shares a similar goal to the Samtools view sub-command, but historically was more performant.  (There is no longer any considerable difference between the two.)  Now Scramble is still supported, but is also a test bed for more experimental CRAM features, such as the CRAM 4.0 version.

A few related tools in io_lib are scram_flagstat, scram_merge, scram_pileup and cram_index.

Download and Installation

Scramble is part of the Staden io_lib package and is available from

Learn and Support

To report any problems, please use the github issue tracker.

License and Citation

Io_lib (and hence Scramble) uses a mixture of BSD and MIT OpenSource licenses.


Sanger Contributors