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Cleanup my pathetic prose. 

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hanna 2009-07-15 21:35:13 +00:00
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@ -16,8 +16,8 @@ Because many tools to analyze next-generation sequencing data access
the data in a very similar way, the GATK can provide a small but the data in a very similar way, the GATK can provide a small but
nearly comprehensive set of traversal types that satisfying the data nearly comprehensive set of traversal types that satisfying the data
access needs of the majority of analysis tools. For example, access needs of the majority of analysis tools. For example,
traversals -Y´by each sequencer read¡ and ´by every read covering traversals "by each sequencer read" and "by every read covering
each locus in a genome¡ are common throughout many tools such as each locus in a genome" are common throughout many tools such as
counting reads, building base quality histograms, reporting average counting reads, building base quality histograms, reporting average
coverage of the genome, and calling SNPs. The small number of these coverage of the genome, and calling SNPs. The small number of these
traversals, shared among many tools enables the core GATK development traversals, shared among many tools enables the core GATK development
@ -52,28 +52,27 @@ intervals on the genome (ByWindow traversal).
Dependencies Dependencies
------------ ------------
The GATK relies on a Java 6-compatible JRE. At the time of this writing, The GATK relies on a Java 6-compatible JRE. At the time of this writing,
the GATK team tests with Sun JRE version 1.6.0_12-b04. the GATK team tests with Sun JRE version 1.6.0_12-b04. Additionally, the
GATK requires as inputs a sorted, indexed BAM file containing aligned reads
and a fasta-format reference with associated dictionary file (.dict)and
index (.fasta.fai).
Additionally, a sorted, indexed BAM file containing aligned reads and a Instructions for preparing input files are available here:
fasta-format reference with associated dictionary file (.dict) and
index (.fasta.fai) are required inputs to the tool.
Instructions for preparing input files are available at the site below:
http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_input_files http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_input_files
An example BAM and fasta are provided in the 'resources' directory of The bundled 'resources' directory contains an example BAM and fasta.
the GATK.
Getting Started Getting Started
--------------- ---------------
The GATK is distributed with a few standard analyses, including PrintReads, The GATK is distributed with a few standard analyses, including PrintReads,
Pileup, and DepthOfCoverage. More information on the included walkers is Pileup, and DepthOfCoverage. More information on the included walkers is
available on the following wiki page: available here:
http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_walkers http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_walkers
To run PrintReads on the included sample data, run the following command: To print the reads of the included sample data, untar the package into
the GenomeAnalysisTK directory and run the following command:
java -jar GenomeAnalysisTK/GenomeAnalysisTK.jar \ java -jar GenomeAnalysisTK/GenomeAnalysisTK.jar \
-T PrintReads \ -T PrintReads \
@ -82,7 +81,6 @@ java -jar GenomeAnalysisTK/GenomeAnalysisTK.jar \
Support Support
------- -------
Documentation for the GATK is available at Documentation for the GATK is available at http://www.broadinstitute.org/gsa/wiki.
http://www.broadinstitute.org/gsa/wiki. For help using or developing For help using the GATK, developing analyses with the GATK, bug reports,
for the GATK, bug reports, or feature requests, please email or feature requests, please email gsadevelopers@broadinstitute.org.
gsadevelopers@broadinstitute.org.