Changes between Version 7 and Version 8 of SNPPipelineTestManual


Ignore:
Timestamp:
Dec 23, 2010 3:19:50 PM (11 years ago)
Author:
freerkvandijk
Comment:

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  • SNPPipelineTestManual

    v7 v8  
    1616* GATK
    1717 - The GATK has several dependancies:
    18  - Ant
     18 - Apache Ant
    1919 - JRE
     20 - Make sure you download the GATK version from the SVN, since this version contains scripts which aren't available in the pre-build version
    2021 - More information to be found here: http://www.broadinstitute.org/gsa/wiki/index.php/Prerequisites & http://www.broadinstitute.org/gsa/wiki/index.php/Downloading_the_GATK
    2122* SAMtools
    2223* Pindel
    2324* FastQC
     25
     26Other less important tools:
     27* To run GATK variant eval using Rscript the following steps need to be executed:
     28 - 1. Add the path to GATK R directory to your .Rprofile (usually this file is in your home directory, otherwise just create it).
     29  - Open your .Rprofile file and add  .libPaths(“/path/to/Sting/R”) to the file
     30 - 2. If you haven't set the path to your R installation execute:
     31  - PATH=$PATH:/path/to/R/bin
     32 - 3.Go to GATK directory, in this case /path/to/Sting
     33  - execute the following command: ant gsalib
    2434
    2535'''__Step 3__''' Configure pipeline