== Resource ==
All source code can be downloaded at http://www.bbmriwiki.nl/svn/ngs_pipelines/

== Procedure ==
__'''Step 1'''__ Obtain datasets

Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen

__'''Step 2'''__ Install tools

You need to install the following tools and set up required index files.

* BWA
 - A patched version can be dowloaded from the SVN using: svn co http://www.bbmriwiki.nl/svn/bwa_45_patched
 - Afterwards run the "make" command
* GATK
 - The GATK has several dependancies:
 - Apache Ant
 - JRE
 - Make sure you download the GATK version from the SVN, since this version contains scripts which aren't available in the pre-build version
 - More information to be found here: http://www.broadinstitute.org/gsa/wiki/index.php/Prerequisites & http://www.broadinstitute.org/gsa/wiki/index.php/Downloading_the_GATK
* SAMtools
* Pindel
* FastQC

Other less important tools:
* To run GATK variant eval using Rscript the following steps need to be executed:
 - 1. Add the path to GATK R directory to your .Rprofile (usually this file is in your home directory, otherwise just create it).
  - Open your .Rprofile file and add  .libPaths(“/path/to/Sting/R”) to the file
 - 2. If you haven't set the path to your R installation execute:
  - PATH=$PATH:/path/to/R/bin
 - 3.Go to GATK directory, in this case /path/to/Sting
  - execute the following command: ant gsalib

'''__Step 3__''' Configure pipeline

Edit pipeline.properties to locate datasets and tools

'''__Step 4__''' Generate pipeline

Run /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts