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Update tool version to 0.0.7 draft
Thu, 28 Feb 2013 15:41:24 -0600, by Jim Johnson
Omit --read_filter param included by default draft
Thu, 28 Feb 2013 15:32:04 -0600, by Jim Johnson
unified_genotyper - add sample_poidy param draft
Thu, 28 Feb 2013 12:45:44 -0600, by Jim Johnson
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set draft
Thu, 28 Feb 2013 12:44:55 -0600, by Jim Johnson
Temporarily use my own copy of samtools - correct name draft
Tue, 19 Feb 2013 21:04:33 -0600, by Jim Johnson
Temporarily use my own copy of samtools until cross dependency support is in release draft
Tue, 19 Feb 2013 20:59:51 -0600, by 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 15:48:46 -0600, by Jim Johnson
Use repository dependency for samtools with corrected revision draft
Mon, 18 Feb 2013 11:17:32 -0600, by Jim Johnson
Use repository dependency for samtools (from main toolshed) draft
Mon, 18 Feb 2013 11:13:47 -0600, by Jim Johnson
Use repository dependency for samtools draft
Mon, 18 Feb 2013 11:01:18 -0600, by Jim Johnson
Add BQSR and plot_pdf_file options to base_recalibrator.xml draft
Fri, 28 Dec 2012 14:15:14 -0600, by Jim Johnson
Replace covariate DinucCovariate with ContextCovariate draft
Fri, 28 Dec 2012 12:34:05 -0600, by Jim Johnson
Remove thread options from base_recalibrator.xml draft
Fri, 28 Dec 2012 12:08:47 -0600, by Jim Johnson
Fix base_recalibrator.xml option: no_standard_covs draft
Fri, 28 Dec 2012 11:50:20 -0600, by Jim Johnson

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