wiki:SNPPipelineTestManual

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.

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

Last modified 7 years ago Last modified on Dec 23, 2010 3:19:50 PM