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

== Procedure ==
__'''Step 1'''__ Obtain datasetsDownload raw BGI FASTQ files from Grid or use the simulated files from Jeroen

__'''Step 2'''__ Install toolsYou need to install the following tools and set up required index files.

 * BWA
 * GATK
 * Pindel

'''__Step 3__''' Configure pipelineEdit pipeline.properties to locate datasets and tools

'''__Step 4__''' Generate pipelineRun /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts