Mercurial > repos > jjohnson > gatk2
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VariantFiltration should not have -nt option since it does not implemnt TreeReducible draft default tipTue, 05 Mar 2013 11:15:13 -0600, by Jim Johnson
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Update options for UnifiedGenotyper p_nonref_model for version 2.3 draftMon, 04 Mar 2013 21:37:30 -0600, by Jim Johnson
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unified_genotyper - indelGap penalty param need to be integer values draftFri, 01 Mar 2013 12:43:41 -0600, by Jim Johnson
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variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set draftThu, 28 Feb 2013 12:44:55 -0600, by Jim Johnson
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Temporarily use my own copy of samtools - correct name draftTue, 19 Feb 2013 21:04:33 -0600, by Jim Johnson
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Temporarily use my own copy of samtools until cross dependency support is in release draftTue, 19 Feb 2013 20:59:51 -0600, by Jim Johnson
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Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values draftMon, 18 Feb 2013 15:48:46 -0600, by Jim Johnson
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Use repository dependency for samtools with corrected revision draftMon, 18 Feb 2013 11:17:32 -0600, by Jim Johnson
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Use repository dependency for samtools (from main toolshed) draftMon, 18 Feb 2013 11:13:47 -0600, by Jim Johnson
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Add BQSR and plot_pdf_file options to base_recalibrator.xml draftFri, 28 Dec 2012 14:15:14 -0600, by Jim Johnson
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Replace covariate DinucCovariate with ContextCovariate draftFri, 28 Dec 2012 12:34:05 -0600, by Jim Johnson
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Remove thread options from base_recalibrator.xml draftFri, 28 Dec 2012 12:08:47 -0600, by Jim Johnson
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Fix base_recalibrator.xml option: no_standard_covs draftFri, 28 Dec 2012 11:50:20 -0600, by Jim Johnson
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remove thread options from indel_realigner.xml draftFri, 28 Dec 2012 11:21:40 -0600, by Jim Johnson
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remove thread options from realigner_target_creator.xml draftFri, 28 Dec 2012 11:08:23 -0600, by Jim Johnson
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Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2 draftThu, 15 Nov 2012 10:17:22 -0600, by Jim Johnson
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Comment out site options from reduce_reads.xml draftTue, 06 Nov 2012 12:07:36 -0600, by Jim Johnson
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Quote the tool_dependencies.xml GATK2_SITE_OPTIONS action text draftFri, 02 Nov 2012 13:47:22 -0500, by Jim Johnson
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tool_dependencies.xml - fix move_file and add symlink draftThu, 01 Nov 2012 14:19:38 -0500, by Jim Johnson
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tool_dependencies.xml - fix move_file and add symlink draftThu, 01 Nov 2012 14:00:40 -0500, by Jim Johnson
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Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml draftThu, 01 Nov 2012 13:44:41 -0500, by Jim Johnson