| Thu, 28 Feb 2013 15:32:04 -0600 |
Jim Johnson |
Omit --read_filter param included by default
draft
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| Thu, 28 Feb 2013 12:45:44 -0600 |
Jim Johnson |
unified_genotyper - add sample_poidy param
draft
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| 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
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| Tue, 19 Feb 2013 21:04:33 -0600 |
Jim Johnson |
Temporarily use my own copy of samtools - correct name
draft
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| 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
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| 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
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| Mon, 18 Feb 2013 11:17:32 -0600 |
Jim Johnson |
Use repository dependency for samtools with corrected revision
draft
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| Mon, 18 Feb 2013 11:13:47 -0600 |
Jim Johnson |
Use repository dependency for samtools (from main toolshed)
draft
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| Mon, 18 Feb 2013 11:01:18 -0600 |
Jim Johnson |
Use repository dependency for samtools
draft
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| Fri, 28 Dec 2012 14:15:14 -0600 |
Jim Johnson |
Add BQSR and plot_pdf_file options to base_recalibrator.xml
draft
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| Fri, 28 Dec 2012 12:34:05 -0600 |
Jim Johnson |
Replace covariate DinucCovariate with ContextCovariate
draft
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| Fri, 28 Dec 2012 12:08:47 -0600 |
Jim Johnson |
Remove thread options from base_recalibrator.xml
draft
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| Fri, 28 Dec 2012 11:50:20 -0600 |
Jim Johnson |
Fix base_recalibrator.xml option: no_standard_covs
draft
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| Fri, 28 Dec 2012 11:21:40 -0600 |
Jim Johnson |
remove thread options from indel_realigner.xml
draft
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| Fri, 28 Dec 2012 11:08:23 -0600 |
Jim Johnson |
remove thread options from realigner_target_creator.xml
draft
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| Thu, 20 Dec 2012 11:01:55 -0600 |
Jim Johnson |
Update tool_dependencies to GATK v 2.3
draft
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| Thu, 15 Nov 2012 10:18:55 -0600 |
Jim Johnson |
Many fixes to haplotype_caller
draft
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| Thu, 15 Nov 2012 10:18:27 -0600 |
Jim Johnson |
base_recalibrator out_puts gatk_report
draft
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| Thu, 15 Nov 2012 10:17:22 -0600 |
Jim Johnson |
Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2
draft
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| Thu, 08 Nov 2012 13:09:56 -0600 |
Jim Johnson |
Remove unneeded params
draft
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| Thu, 08 Nov 2012 11:50:01 -0600 |
Jim Johnson |
Fix output filters
draft
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| Thu, 08 Nov 2012 10:55:32 -0600 |
Jim Johnson |
Add help to HaplotypeCaller
draft
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| Thu, 08 Nov 2012 10:38:18 -0600 |
Jim Johnson |
Add HaplotypeCaller
draft
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| Tue, 06 Nov 2012 12:07:36 -0600 |
Jim Johnson |
Comment out site options from reduce_reads.xml
draft
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