wiki:SNPPipelineTestManual

Version 1 (modified by Leon Mei, 14 years ago) (diff)

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Resource

All source code can be downloaded at​http://www.bbmriwiki.nl/svn/ngs_pipelines/ 

Procedure

  1. ==== Obtain datasets ====

Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen

  1. ==== Install tools  ====
  • BWA
  • GATK
  • Picart
  1. ==== Configure pipeline  ====

Edit pipeline.properties to locate datasets and tools

  1. ==== Generate pipeline ====

Run /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts