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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
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aaron 2009-03-22 20:10:17 +00:00
parent 02556ce4a6
commit 09d605bb37
2 changed files with 2 additions and 2 deletions
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doc/GATK_Hello_World.tex
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@ -99,8 +99,8 @@ To run the walker:
\begin{verbatim} \begin{verbatim}
mkdir $STING_HOME/dist/walkers mkdir $STING_HOME/dist/walkers
java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \ java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \
INPUT_FILE=/broad/1KG/legacy_data/trio/na12878.bam \ -I /broad/1KG/legacy_data/trio/na12878.bam -T Hello \
ANALYSIS_NAME=Hello L=chr1:10000000-10000100 -L chr1:10000000-10000100 -l INFO
\end{verbatim} \end{verbatim}
This command will run the walker across a subsection of chromosome 1, operating on This command will run the walker across a subsection of chromosome 1, operating on
reads which align to that subsection. reads which align to that subsection.