wiki:SNPPipelineTestManual

Version 4 (modified by Leon Mei, 11 years ago) (diff)

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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
  • 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