Changes between Version 4 and Version 5 of SNPPipelineTestManual


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Timestamp:
Dec 16, 2010 3:54:34 PM (14 years ago)
Author:
Leon Mei
Comment:

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  • SNPPipelineTestManual

    v4 v5  
    33
    44== Procedure ==
    5  * __'''Step 1'''__ Obtain datasets
     5__'''Step 1'''__ Obtain datasetsDownload raw BGI FASTQ files from Grid or use the simulated files from Jeroen
    66
    7   Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen
    8 
    9  * __'''Step 2'''__ Install tools
    10 
    11   You need to install the following tools and set up required index files.
     7__'''Step 2'''__ Install toolsYou need to install the following tools and set up required index files.
    128
    139 * BWA
    1410 * GATK
    15  * Picart
     11 * Pindel
    1612
     13'''__Step 3__''' Configure pipelineEdit pipeline.properties to locate datasets and tools
    1714
    18  * '''__Step 3__''' Configure pipeline
    19 
    20   Edit pipeline.properties to locate datasets and tools
    21 
    22  * '''__Step 4__''' Generate pipeline
    23 
    24   Run /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts
     15'''__Step 4__''' Generate pipelineRun /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts