Changes between Version 6 and Version 7 of SNPPipelineTestManual


Ignore:
Timestamp:
Dec 23, 2010 3:05:24 PM (14 years ago)
Author:
freerkvandijk
Comment:

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  • SNPPipelineTestManual

    v6 v7  
    1111You need to install the following tools and set up required index files.
    1212
    13  * BWA
    14  * GATK
    15  * Pindel
     13* BWA
     14 - A patched version can be dowloaded from the SVN using: svn co http://www.bbmriwiki.nl/svn/bwa_45_patched
     15 - Afterwards run the "make" command
     16* GATK
     17 - The GATK has several dependancies:
     18 - Ant
     19 - JRE
     20 - 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
     21* SAMtools
     22* Pindel
     23* FastQC
    1624
    1725'''__Step 3__''' Configure pipeline