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Authors: Márton Münz, Elise Ruark, Nazneen Rahman, Gerton Lunter, ...
Description: The OpEx (Optimised Exome) pipeline has been developed through a collaboration between ICR and OGC. It includes a fixed implementation of alignment, quality control, variant calling and annotation tools optimised for individual or multiple exome sequencing analysis in the research or clinical setting.



.Capabilities: The OpEx pipeline can be run with a single command and requires FASTQ files to return a tab-separated text file containing clinically annotated substitution and indel variants in an individual. OpEx is running independently at the sample level, providing similar performance for any number of samples.
The OpEx paper is currently in preparation. In the meantime, please reference this site, with the following text: …. (2015) OpEx: optimised pipeline for exome sequencing analysis in the research or clinical setting (
Downloads: The latest stable version (v1.0.0) of OpEx can be downloaded here.
Documentation: The OpEx documentation can be downloaded here and is also included in the tgz package above.
Dependencies: OpEx runs on Linux. It requires Python 2.7.5 or later (with the Pysam module version 0.7.7 or later installed) and Java 1.6.
Installation: To install OpEx, simply download and unpack the tgz file, and run the installation script ( in the opex-v1.0.0 directory. For different modes of installation and further details, see the documentation. Once the script is finished, the OpEx pipeline is ready to run.
Running OpEx:

OpEx can be run with the following command:

/path/to/opex/ -f R1.fastq,R2.fastq -b panel.bed -n sample

You have to specify the paired-end FASTQ files (-f), a unique sample name (-n) and, optionally, a BED file (-b) defining the targeted regions of interest. See more details in the Documentation.

User Group

Join the OpEx User Group on Google Groups - a forum for discussing bug-reports, feature requests, suggestions or any issues related to OpEx.

Please send all bug reports, comments and feature requests to the OpEx User Group on Google Groups or to