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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="gatk" version="2.3">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.3-9-gdcdccbb.tar.bz2</action>
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7 <action type="move_file">
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8 <source>GenomeAnalysisTKLite.jar</source>
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9 <destination>$INSTALL_DIR</destination>
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10 </action>
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11 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
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12 <action type="move_file">
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13 <source>GenomeAnalysisTK.jar</source>
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14 <destination>$INSTALL_DIR</destination>
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15 </action>
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16 <action type="set_environment">
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17 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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18 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--phone_home STANDARD"</environment_variable>
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19 <environment_variable name="GATK2_NUM_THREADS" action="set_to">"--num_threads 4"</environment_variable>
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20 <environment_variable name="GATK2_NUM_CPU_THREADS" action="set_to">"--num_cpu_threads_per_data_thread 3"</environment_variable>
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21 </action>
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22 </actions>
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23 </install>
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24 <readme>
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25 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed:
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26
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27 haplotypecaller
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28 HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an
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29 active region.
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30 HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files.
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31
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32 reducereads
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33 CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads
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34 metrics.
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35 ReduceReads Reduces the BAM file using read based compression that keeps only essential information
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36 for variant calling
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37
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38
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39 See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details.
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40 The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download
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41 and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar
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42
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43 The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified
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44 for the local installation.
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45
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46 </readme>
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47 </package>
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48 </tool_dependency>
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