Socrates - SOft Clip re-alignment To idEntify Structural variants

Developed by Arthur Hsu, Jan Schroeder and Tony Papenfuss


Socrates is a highly efficient and sensitive method for detecting genomic rearrangements in tumours that utilises split-read data. Socrates features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It annotates micro-homologies and untemplated sequence insertions at the breakpoint. It takes advantage of parallelism for efficient use of resources.

The latest version of Socrates (version 1.1+) is available from github. It requires Java 1.8. Older versions are also available. They will run with older versions of Java.

If you find Socrates useful, please cite our publication:

Schroeder J, Hsu A, Boyle SE, MacIntyre G, Cmero M, Tothill RW, Johnstone RW, Shackleton M, Papenfuss AT. Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. Bioinformatics 2014, 30:8, 1064-1072.

Many of the ideas of SOCRATES have now been re-implemented and extended in GRIDSS.


Socrates makes use of external libraries that are licensed under Apache License Version 2.0 and The MIT License. The GNU General Public License Version 3 (GPLv3) applies to the Socrates programs itself. By downloading or using this program you are also agreeing to these licenses.

Socrates is a pure split read-based breakpoint caller, which is designed to be fast and sensitive. It is a highly efficient for detecting genomic rearrangements in tumours, but requires downstream filtering of calls by the user.