111 lines
3.8 KiB
TeX
Executable File
111 lines
3.8 KiB
TeX
Executable File
\documentclass[11pt,fullpage]{article}
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\usepackage[urlcolor=blue,colorlinks=true]{hyperref}
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\oddsidemargin 0.0in
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\textwidth 6.5in
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\begin{document}
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\title{Getting Started with the Genome Analysis Toolkit (GATK)}
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\author{Matt Hanna}
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\date{Created March 16, 2009\\ Updated \today}
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\maketitle
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\section{Build Prerequisites}
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GATK requires JDK 1.6 and Ant 1.7.1 to compile.
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\section{Getting and Building the Source}
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GATK is located in the Sting svn repository, and
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compiles using a build.xml in the root directory.
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Download and build the source as follows:
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\begin{verbatim}
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svn co https://svnrepos/Sting/trunk Sting
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cd Sting
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ant
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\end{verbatim}
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\section{Getting Started}
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The core concept behind GATK is the walker, a class that implements the
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three core operations: filtering, mapping, and reducing.
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\begin{description}
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\item [filter] reduces the size of the dataset by applying a predicate.
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\item [map] Applies a function to each individual element in a dataset,
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effectively 'mapping' it to a new element.
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\item [reduce] Inductively combines the elements of a list. The base
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case is supplied by the reduceInit() function, and the inductive step
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is performed by the reduce() function.
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\end{description}
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Users of the GATK will provide a walker to run their analyses. The engine
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will produce a result by first filtering the dataset, running a map operation,
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and finally reducing the map operation to a single result.
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\section{Creating a Walker}
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To be loaded by GATK, the walker must satisfy the following properties:
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\begin{enumerate}
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\item It must be a loose class, not packaged into a jar file.
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\item It must be in the unnamed package (in other words, the source
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should not start with a package declaration).
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\item It must subclass one of the basic walkers in the
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org.broadinstitute.sting.gatk.walkers package: ReadWalker or
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LociWalker.
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\item It must live in the directory \$STING\_HOME/dist/walkers.
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\end{enumerate}
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\section{Example}
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This walker will print output for each read it sees, eventually computing the
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total number of reads by mapping every read to 1 and summing all the 1s to
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realize the total number of reads.
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\begin{samepage}
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Copy the following text into the file \$STING\_HOME/dist/walkers/HelloWalker.java:
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\begin{verbatim}
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.LocusContext;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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/**
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* Define a class extending from ReadWalker with types
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* <MapType,ReduceType>.
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*/
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public class HelloWalker extends ReadWalker<Integer,Long> {
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private Long currentRead = 0L;
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// Maps each read to the value 1.
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public Integer map(LocusContext context, SAMRecord read) {
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System.out.printf("Hello read %d%n", ++currentRead );
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return 1;
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}
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// Provides an initial value for the reduce function.
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public Long reduceInit() { return 0L; }
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// Defines how to compute the reduction given a value in the list.
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public Long reduce(Integer value, Long sum) {
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return sum + value;
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}
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}
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\end{verbatim}
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\end{samepage}
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To compile the walker:
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\begin{verbatim}
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setenv CLASSPATH $STING_HOME/dist/GenomeAnalysisTK.jar:$STING_HOME/dist/sam-1.0.jar
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javac HelloWalker.java
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\end{verbatim}
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To run the walker:
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\begin{verbatim}
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mkdir $STING_HOME/dist/walkers
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java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \
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-R/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta \
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-I /broad/1KG/legacy_data/trio/na12878.bam -T Hello \
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-L chr1:10000000-10000100 -l WARN
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\end{verbatim}
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This command will run the walker across a subsection of chromosome 1, operating on
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reads which align to that subsection. If you'd like to see more information from the GATK
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on what it's doing, you can change the logging level (-l) to INFO.
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\end{document}
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