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annotate README @ 21:6e641ee02851 draft

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Fix base_recalibrator.xml option: no_standard_covs
author Jim Johnson <jj@umn.edu>
date Fri, 28 Dec 2012 11:50:20 -0600
parents 7533db8dfb5b
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1 The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be
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2 copied into the tool-data directory. The file tool_data_table_conf.xml must
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3 be edited to include references to these two new files.
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7533db8dfb5b Update tool_dependencies to GATK v 2.3
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5 GATK can be installed via tool_dependencies.
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6 This will install GenomeAnalysisTKLite.jar from ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/
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7 and create a symbolic link from GenomeAnalysisTK.jar to GenomeAnalysisTKLite.jar
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9 If you have a full licensed copy of GenomeAnalysisTK.jar, change the GenomeAnalysisTK.jar symbolic link
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10 in the installation directory to point to your licensed copy.
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12 Two environment variables: GATK2_SITE_OPTIONS and GATK2_THREAD_OPTIONS are also set in the tool_dependencies env.sh file.
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13 You can alter the value of those variables for your site.
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14 $ cat tool_dependencies/gatk/2.2/*/gatk2/*/env.sh
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15 GATK2_PATH=/Users/jj/gxt/gxt/tool_dependencies/gatk/2.2/jimmy/gatk2/288cdae6bd9c; export GATK2_PATH
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16 GATK2_SITE_OPTIONS="--phone_home STANDARD"; export GATK2_SITE_OPTIONS
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17 GATK2_THREAD_OPTIONS="--num_threads 4 --num_cpu_threads_per_data_thread 3"; export GATK2_THREAD_OPTIONS
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