Changes between Version 5 and Version 6 of SNPPipelineTestManual


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Timestamp:
Dec 16, 2010 3:55:00 PM (14 years ago)
Author:
Leon Mei
Comment:

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  • SNPPipelineTestManual

    v5 v6  
    33
    44== Procedure ==
    5 __'''Step 1'''__ Obtain datasetsDownload raw BGI FASTQ files from Grid or use the simulated files from Jeroen
     5__'''Step 1'''__ Obtain datasets
    66
    7 __'''Step 2'''__ Install toolsYou need to install the following tools and set up required index files.
     7Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen
     8
     9__'''Step 2'''__ Install tools
     10
     11You need to install the following tools and set up required index files.
    812
    913 * BWA
    … …  
    1115 * Pindel
    1216
    13 '''__Step 3__''' Configure pipelineEdit pipeline.properties to locate datasets and tools
     17'''__Step 3__''' Configure pipeline
    1418
    15 '''__Step 4__''' Generate pipelineRun /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts
     19Edit pipeline.properties to locate datasets and tools
     20
     21'''__Step 4__''' Generate pipeline
     22
     23Run /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts