Changes between Version 1 and Version 2 of SNPPipelineTestManual


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Timestamp:
Dec 16, 2010 3:32:55 PM (14 years ago)
Author:
Leon Mei
Comment:

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  • SNPPipelineTestManual

    v1 v2  
    11== Resource ==
    2 All source code can be downloaded at[http://www.bbmriwiki.nl/svn/ngs_pipelines/ http://www.bbmriwiki.nl/svn/ngs_pipelines/] 
     2All source code can be downloaded at[http://www.bbmriwiki.nl/svn/ngs_pipelines/ http://www.bbmriwiki.nl/svn/ngs_pipelines/]
    33
    44== Procedure ==
    5  1. ==== Obtain datasets ====
    6 Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen
     5 * __'''Step 1'''__ Obtain datasets
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    87
    9  1. ==== Install tools  ====
     8
     9  Download raw BGI FASTQ files from Grid or use the simulated files from Jeroen
     10
     11 * __'''Step 2'''__ Install tools
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    1113   * BWA
    1214   * GATK
    1315   * Picart
    14  1. ==== Configure pipeline  ====
    15 Edit pipeline.properties to locate datasets and tools
    1616
     17 * '''__Step 3__''' Configure pipeline
    1718
    18  1. ==== Generate pipeline ====
    19 Run /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts
     19  Edit pipeline.properties to locate datasets and tools
     20
     21 * '''__Step 4__''' Generate pipeline
     22
     23  Run /src/ngsscriptgenerator/NGSScriptGenerator.java to generate the pipeline scripts