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
  • A patched version can be dowloaded from the SVN using: svn co ​http://www.bbmriwiki.nl/svn/bwa_45_patched
  • Afterwards run the "make" command
• GATK
  • The GATK has several dependancies:
  • Apache Ant
  • JRE
  • Make sure you download the GATK version from the SVN, since this version contains scripts which aren't available in the pre-build version
  • More information to be found here: ​http://www.broadinstitute.org/gsa/wiki/index.php/Prerequisites & ​http://www.broadinstitute.org/gsa/wiki/index.php/Downloading_the_GATK
• SAMtools
• Pindel
• FastQC

Other less important tools:

• To run GATK variant eval using Rscript the following steps need to be executed:
  • 1. Add the path to GATK R directory to your .Rprofile (usually this file is in your home directory, otherwise just create it).
    • Open your .Rprofile file and add .libPaths(“/path/to/Sting/R”) to the file
  • 2. If you haven't set the path to your R installation execute:
    • PATH=$PATH:/path/to/R/bin
  • 3.Go to GATK directory, in this case /path/to/Sting
    • execute the following command: ant gsalib

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