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Tue, 05 Mar 2013 11:15:13 -0600 Jim Johnson VariantFiltration should not have -nt option since it does not implemnt TreeReducible draft default tip
Mon, 04 Mar 2013 21:37:30 -0600 Jim Johnson Update options for UnifiedGenotyper p_nonref_model for version 2.3 draft
Fri, 01 Mar 2013 12:43:41 -0600 Jim Johnson unified_genotyper - indelGap penalty param need to be integer values draft
Fri, 01 Mar 2013 08:07:56 -0600 Jim Johnson Fix commandline template draft
Fri, 01 Mar 2013 07:52:02 -0600 Jim Johnson Fix default read filter screening draft
Thu, 28 Feb 2013 15:41:24 -0600 Jim Johnson Update tool version to 0.0.7 draft
Thu, 28 Feb 2013 15:32:04 -0600 Jim Johnson Omit --read_filter param included by default draft
Thu, 28 Feb 2013 12:45:44 -0600 Jim Johnson unified_genotyper - add sample_poidy param draft
Thu, 28 Feb 2013 12:44:55 -0600 Jim Johnson variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set draft
Tue, 19 Feb 2013 21:04:33 -0600 Jim Johnson Temporarily use my own copy of samtools - correct name draft
Tue, 19 Feb 2013 20:59:51 -0600 Jim Johnson Temporarily use my own copy of samtools until cross dependency support is in release draft
Mon, 18 Feb 2013 15:48:46 -0600 Jim Johnson Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values draft
Mon, 18 Feb 2013 11:17:32 -0600 Jim Johnson Use repository dependency for samtools with corrected revision draft
Mon, 18 Feb 2013 11:13:47 -0600 Jim Johnson Use repository dependency for samtools (from main toolshed) draft
Mon, 18 Feb 2013 11:01:18 -0600 Jim Johnson Use repository dependency for samtools draft
Fri, 28 Dec 2012 14:15:14 -0600 Jim Johnson Add BQSR and plot_pdf_file options to base_recalibrator.xml draft
Fri, 28 Dec 2012 12:34:05 -0600 Jim Johnson Replace covariate DinucCovariate with ContextCovariate draft
Fri, 28 Dec 2012 12:08:47 -0600 Jim Johnson Remove thread options from base_recalibrator.xml draft
Fri, 28 Dec 2012 11:50:20 -0600 Jim Johnson Fix base_recalibrator.xml option: no_standard_covs draft
Fri, 28 Dec 2012 11:21:40 -0600 Jim Johnson remove thread options from indel_realigner.xml draft
Fri, 28 Dec 2012 11:08:23 -0600 Jim Johnson remove thread options from realigner_target_creator.xml draft
Thu, 20 Dec 2012 11:01:55 -0600 Jim Johnson Update tool_dependencies to GATK v 2.3 draft
Thu, 15 Nov 2012 10:18:55 -0600 Jim Johnson Many fixes to haplotype_caller draft
Thu, 15 Nov 2012 10:18:27 -0600 Jim Johnson base_recalibrator out_puts gatk_report draft
Thu, 15 Nov 2012 10:17:22 -0600 Jim Johnson Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2 draft
Thu, 08 Nov 2012 13:09:56 -0600 Jim Johnson Remove unneeded params draft
Thu, 08 Nov 2012 11:50:01 -0600 Jim Johnson Fix output filters draft
Thu, 08 Nov 2012 10:55:32 -0600 Jim Johnson Add help to HaplotypeCaller draft
Thu, 08 Nov 2012 10:38:18 -0600 Jim Johnson Add HaplotypeCaller draft
Tue, 06 Nov 2012 12:07:36 -0600 Jim Johnson Comment out site options from reduce_reads.xml draft
Tue, 06 Nov 2012 11:48:49 -0600 Jim Johnson Fix dir path to GenomeAnalysisTKLite.jar draft
Tue, 06 Nov 2012 11:41:15 -0600 Jim Johnson Update tool_dependencies.xml draft
Tue, 06 Nov 2012 11:23:22 -0600 Jim Johnson Cleanup reduce_reads.xml draft
Tue, 06 Nov 2012 10:32:16 -0600 Jim Johnson ReduceReads added draft
Fri, 02 Nov 2012 13:47:22 -0500 Jim Johnson Quote the tool_dependencies.xml GATK2_SITE_OPTIONS action text draft
Thu, 01 Nov 2012 14:30:06 -0500 Jim Johnson tool_dependencies.xml - fix set_environment draft
Thu, 01 Nov 2012 14:19:38 -0500 Jim Johnson tool_dependencies.xml - fix move_file and add symlink draft
Thu, 01 Nov 2012 14:00:40 -0500 Jim Johnson tool_dependencies.xml - fix move_file and add symlink draft
Thu, 01 Nov 2012 13:44:41 -0500 Jim Johnson Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml draft
Thu, 01 Nov 2012 13:53:22 -0400 jjohnson Uploaded draft
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