diff --git a/doc/GATK_Hello_World.pdf b/doc/GATK_Hello_World.pdf index baad18678..4a1aefc9e 100755 Binary files a/doc/GATK_Hello_World.pdf and b/doc/GATK_Hello_World.pdf differ diff --git a/doc/GATK_Hello_World.tex b/doc/GATK_Hello_World.tex index f20ef486b..1a5c25431 100755 --- 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.