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DeNovoCheck
==================
Inheritance analysis for NGS trio data  
------------------

DeNovoCheck is intended to be used for inheritance analysis in NGS tio data.
For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. 
The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants. 

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Release
==================
 Version: 2.0.0	
 Date:    31-March-2013
 License: GNU GPLv3

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Pre-requisites
==================
* JRE 6 / JDK 1.6 or higher
    * <http://www.oracle.com/technetwork/java/index.html>

* Samtools v. 1.16 or higher
    * <http://samtools.sourceforge.net/>
    * svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools  

Please ensure that **javac -version** and **java -version** give the same version result.

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Installation
==================
Please ensure that all Pre-required software (listed above) is installed.

1. Visit <https://sourceforge.net/projects/denovocheck/files/>
2. Download DeNovoCheck_DATE.tar.gz
3. Unpack DeNovoCheck.tar.gz to a **Directory**

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Running
==================
DeNovoCheck can be run using a properties file or using command line arguments:

~~~~~~
:::shell
DeNovoCheck.jar -properties /path/properties_file.txt
~~~~~~
Runs the program with a properties file.

~~~~~~
:::shell
DeNovoCheck.jar -parameter1 value1 -parameter2 value2 etc...
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Uses commandline specified paramters to run DNC.


If execute rights are not set or additional java options need to be passed, 
please call the program as shown below:

~~~~~~
:::shell
java -Xms500m -Xmx500m -jar Directory/DeNovoCheck.jar -option1 argument1
~~~~~~


Exmaples of what properties to set are provided on the command line and in the default properties file generated by the program when calling it without arguments. More detailed explenations are given on the project website.


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Contact
==================
* Project URL: <https://sourceforge.net/projects/denovocheck/>
+ Developer contact: <denovocheck@users.sourceforge.net>
+ Bug reporting: <https://sourceforge.net/p/denovocheck/tickets/>

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Developer
==================
 Joep de Ligt
 UMCN St Radboud
 Genomic Disorders Nijmegen
 http://www.genomicdisorders.nl/
Source: README, updated 2013-04-03