Version 5 (modified by Leon Mei, 11 years ago) (diff)



All source code can be downloaded at


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 to locate datasets and tools

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