diff --git a/doc/GATK_Hello_World.pdf b/doc/GATK_Hello_World.pdf index 0331cc804..ae3a4d276 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 0651ab94c..1e752db00 100755 --- a/doc/GATK_Hello_World.tex +++ b/doc/GATK_Hello_World.tex @@ -8,7 +8,7 @@ \title{Getting Started with the Genome Analysis Toolkit (GATK)} \author{Matt Hanna} -\date{16 Mar 2009} +\date{Created March 16, 2009\\ Updated \today} \maketitle \section{Build Prerequisites} @@ -99,10 +99,12 @@ To run the walker: \begin{verbatim} mkdir $STING_HOME/dist/walkers java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \ + -R/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta \ -I /broad/1KG/legacy_data/trio/na12878.bam -T Hello \ - -L chr1:10000000-10000100 -l INFO + -L chr1:10000000-10000100 -l WARN \end{verbatim} 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. If you'd like to see more information from the GATK +on what it's doing, you can change the logging level (-l) to INFO. \end{document}