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