== 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
 * GATK
 * Picart


 * '''__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