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The OpEx pipeline

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.

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.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.
Reference:
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 (www.well.ox.ac.uk/opex).
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 (install.py) in the opex-v1.0.0 directory. For different modes of installation and further details, see the documentation. Once the install.py script is finished, the OpEx pipeline is ready to run.
Running OpEx:

OpEx can be run with the following command:

/path/to/opex/opex.py -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.
Contact:
Please send all bug reports, comments and feature requests to the OpEx User Group on Google Groups or to opex-user-group@googlegroups.com.