89 lines
4.2 KiB
Plaintext
89 lines
4.2 KiB
Plaintext
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The Genome Analysis Toolkit (GATK)
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Copyright (c) 2009 The Broad Institute
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Overview
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--------
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The Genome Analysis Toolkit (GATK) is a structured programming
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framework designed to enable rapid development of efficient and robust
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analysis tools for next-generation DNA sequencers. The GATK solves
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the data management challenge by separating data access patterns from
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analysis algorithms, using the functional programming philosophy of
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Map/Reduce. Consequently, the GATK is structured into data traversals
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and data walkers that interact through a programming contract in which
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the traversal provides a series of units of data to the walker, and
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the walker consumes each datum to generate an output for each datum.
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Because many tools to analyze next-generation sequencing data access
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the data in a very similar way, the GATK can provide a small but
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nearly comprehensive set of traversal types that satisfying the data
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access needs of the majority of analysis tools. For example,
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traversals -Y<>by each sequencer read<61> and <20>by every read covering
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each locus in a genome<6D> are common throughout many tools such as
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counting reads, building base quality histograms, reporting average
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coverage of the genome, and calling SNPs. The small number of these
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traversals, shared among many tools enables the core GATK development
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team to optimize such traversals for correctness, stability, CPU
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performance, memory footprint, and in many cases to even automatically
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parallelize calculations. Moreover, since the traversal engine
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encapsulates the complexity of efficiently accessing the
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next-generation sequencing data, researchers and developers are free
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to focus on their specific analysis algorithms. This not only vastly
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improves productivity of the developers, who can quickly write new
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analyses, but also results in tools that are efficient and robust and
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can benefit from improvement to a common data management engine.
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Capabilities
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------------
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The GenomeAnalysisTK development environment is currently provided as
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a platform-independent Java programming language library. The core
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system works with the nascent standard Sequence Alignment/Map (SAM)
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format to represent reads using a production-quality SAM library
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developed at the Broad. The system can access a variety of metadata
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files such as dbSNP, Hapmap, RefSeq as well as work with genotype and
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SNP files in GLF, Geli, and other common formats. The core system
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handles read data from Illumina/Solexa, SOLiD, and Roche/454. The
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current GATK engine can process all of the 1000 genomes data
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representing ~5Tb of data from these three technologies produced from
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multiple sequencing centers and aligned to the human reference genome
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with multiple aligners. The GATK currently provides traversals by
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each read (ByRead traversal), by all reads covering each locus in the
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genome (ByLoci traversal), and by all reads within pre-specified
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intervals on the genome (ByWindow traversal).
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Dependencies
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------------
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The GATK relies on a Java 6-compatible JRE. At the time of this writing,
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the GATK team tests with Sun JRE version 1.6.0_12-b04.
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Additionally, a sorted, indexed BAM file containing aligned reads and a
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fasta-format reference with associated dictionary file (.dict) and
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index (.fasta.fai) are required inputs to the tool.
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Instructions for preparing input files are available at the site below:
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http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_input_files
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An example BAM and fasta are provided in the 'resources' directory of
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the GATK.
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Getting Started
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---------------
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The GATK is distributed with a few standard analyses, including PrintReads,
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Pileup, and DepthOfCoverage. More information on the included walkers is
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available on the following wiki page:
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http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_walkers
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To run PrintReads on the included sample data, run the following command:
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java -jar GenomeAnalysisTK/GenomeAnalysisTK.jar \
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-T PrintReads \
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-R GenomeAnalysisTK/resources/exampleFASTA.fasta \
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-I GenomeAnalysisTK/resources/exampleBAM.bam
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Support
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-------
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Documentation for the GATK is available at
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http://www.broadinstitute.org/gsa/wiki. For help using or developing
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for the GATK, bug reports, or feature requests, please email
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gsadevelopers@broadinstitute.org.
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