Computational Biology Lab

Download PRISM(source code included):

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PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

PRISM and PRISM_CTX were originally designed and written by Michael Brudno and Yue Jiang, The original PRISM publication can be found here.

The authors may be contacted via e-mail at: prism at

Additional information is available in the PRISM README file and PRISM_CTX README file.


December 29, 2013 -

PRISM 1.1.6, README file and program usage updated. PRISM works on one chromosome at one time. It accepts single chromosome reference file e.g. chr1.fa not whole genome reference e.g. hg19.fa. This was not metioned in the README file and the program usage.

September 5, 2012 -

PRISM 1.1.6, a spelling error in is fixed. The max accepted read length is set to 500bp. Removed awk bit operation ("and" function) in

June 13, 2012 -

PRISM 1.1.5, Made tiny inside parameters adjustment. In the README file section 6 illustrates how to use other tools' result as cluster files instead of CNVer. In the which is a replacement of "smapper bwasam2tracks" command the discordant pairs who have an alternative concordant mapping are no longer considered during the cluster. Only the best level alignment are used in the cluster step the suboptimal level alignment is ignored. This holds for the scripts "" in all versions who contain it.

February 23, 2012 -

PRISM 1.1.4, A bug of generating invalid CIGARs for inversions is fixed. All the programs for sv calling are rewritten in python. Now the sv loci file have more fields which means users are able to filter the svs with more infomation, see README for details.

February 15, 2012 -

PRISM_CTX 1.0.1, this is a tool for detecting inter-chromosome trans-location events based on the same method of PRISM.

November 28, 2011 -

PRISM 1.1.2, a new script "" added under tookit folder. This script takes the split mapping sam file and SV calling loci file as input and screens out the split reads that support a called SV.

October 19, 2011 -

PRISM 1.1.1, the first public release, is now available. Use the links on the left to download source code and pre-compiled static binaries for i686 and x86_64 platforms (Linux 2.6).