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
• Pindel

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