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RDXplorer at a glance
What is RDXplorer
The RDXplorer (Read Depth eXplorer) is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group (see Publications). The read depth coverage is estimated in non-overlapping intervals (100bp Windows) across an individual genome based on the pileup generated by SAMTools.
Source code, supporting files and user manual are freely available for download for academic and non-profit use.
Beta Release, Version 3.2, Latest update has been uploaded on May 24, 2011.
What is new in the latest update
As per multiple user's requests, it is now possible to select specified chromosome for analysis
Operating SystemLINUX/UNIX/MAC OSX
EnvironmentStandalone machine or HPCC. Possible run modes:
InputRDXplorer accepts the BAM files. Current version accepth HG18 and HG19 builds. The user specifies this at runtime. Default is HG19. Please note!
OutputFor each chromosome found in the BAM file, the following output is generated:
The current version is Python/R hybrid and relies on the following technologies:
One Time Configuration Before You Use
Before you use, please edit 2 lines at "globals.py" according to local specifications. You must specify full path to SAMTools (even it is on your path). This makes your life much easier if you decide to submit it to HPCC to process multiple BAM files at a time.
To run open "run.sh" and change parameters according to your bam file location. This shell is very minimalistic, keeping in mind that evryone will be using RDXplorer differently (see ENVIRONMENT). It can be easily adopted to be called programmatically from your own python program or shell script.
To see the list of accepthed arguments and their types, please see the README file or issue "python rdxplorer.py" (no arguments) command
Performance and Memory Requirements4 GB of RAM is a recommended minimum. Adding more memory will improve performance.
Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009 Sep;19(9):1586-92. Epub 2009 Aug 5. PubMed PMID: 19657104; PubMed Central PMCID: PMC2752127.