wiki:SNPPipelineTestManual

Version 5 (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 datasetsDownload raw BGI FASTQ files from Grid or use the simulated files from Jeroen

Step 2 Install toolsYou need to install the following tools and set up required index files.

  • BWA
  • GATK
  • Pindel

Step 3 Configure pipelineEdit pipeline.properties to locate datasets and tools

Step 4 Generate pipelineRun /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts