Changes between Version 7 and Version 8 of SNPPipelineTestManual

Timestamp:

Dec 23, 2010 3:19:50 PM (14 years ago)

Author:

freerkvandijk

Comment:

--

SNPPipelineTestManual

@@ -16 +16 @@
 * GATK
  - The GATK has several dependancies:
- - Ant
+ - Apache Ant
  - JRE
+ - Make sure you download the GATK version from the SVN, since this version contains scripts which aren't available in the pre-build version
  - 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
 * SAMtools
 * Pindel
 * FastQC
+
+Other less important tools:
+* To run GATK variant eval using Rscript the following steps need to be executed:
+ - 1. Add the path to GATK R directory to your .Rprofile (usually this file is in your home directory, otherwise just create it).
+  - Open your .Rprofile file and add  .libPaths(“/path/to/Sting/R”) to the file
+ - 2. If you haven't set the path to your R installation execute:
+  - PATH=$PATH:/path/to/R/bin
+ - 3.Go to GATK directory, in this case /path/to/Sting
+  - execute the following command: ant gsalib
 
 '''__Step 3__''' Configure pipeline