Changed how the example walker gets run, I'm about to check in the GNU style command line args.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@143 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-22 20:10:17 +00:00 · 2009-03-22 20:10:17 +00:00 · 09d605bb37
parent 02556ce4a6
commit 09d605bb37
2 changed files with 2 additions and 2 deletions
--- a/doc/GATK_Hello_World.pdf
+++ b/doc/GATK_Hello_World.pdf
--- a/doc/GATK_Hello_World.tex
+++ b/doc/GATK_Hello_World.tex
@ -99,8 +99,8 @@ To run the walker:
 \begin{verbatim}
 mkdir $STING_HOME/dist/walkers
 java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \
-     INPUT_FILE=/broad/1KG/legacy_data/trio/na12878.bam \
-     ANALYSIS_NAME=Hello L=chr1:10000000-10000100
+     -I /broad/1KG/legacy_data/trio/na12878.bam -T Hello \
+     -L chr1:10000000-10000100 -l INFO
 \end{verbatim}
 This command will run the walker across a subsection of chromosome 1, operating on 
 reads which align to that subsection.