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

== Procedure ==
 1. ==== Obtain datasets ====
Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen


 1. ==== Install tools  ====

   * BWA
   * GATK
   * Picart
 1. ==== Configure pipeline  ====
Edit pipeline.properties to locate datasets and tools


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