| 2013-03-05 |
Jim Johnson |
VariantFiltration should not have -nt option since it does not implemnt TreeReducible
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| 2013-03-05 |
Jim Johnson |
Update options for UnifiedGenotyper p_nonref_model for version 2.3
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| 2013-03-01 |
Jim Johnson |
unified_genotyper - indelGap penalty param need to be integer values
draft
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| 2013-03-01 |
Jim Johnson |
Fix commandline template
draft
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| 2013-03-01 |
Jim Johnson |
Fix default read filter screening
draft
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| 2013-02-28 |
Jim Johnson |
Update tool version to 0.0.7
draft
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| 2013-02-28 |
Jim Johnson |
Omit --read_filter param included by default
draft
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| 2013-02-28 |
Jim Johnson |
unified_genotyper - add sample_poidy param
draft
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| 2013-02-28 |
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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| 2013-02-20 |
Jim Johnson |
Temporarily use my own copy of samtools - correct name
draft
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| 2013-02-20 |
Jim Johnson |
Temporarily use my own copy of samtools until cross dependency support is in release
draft
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| 2013-02-18 |
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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| 2013-02-18 |
Jim Johnson |
Use repository dependency for samtools with corrected revision
draft
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| 2013-02-18 |
Jim Johnson |
Use repository dependency for samtools (from main toolshed)
draft
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| 2013-02-18 |
Jim Johnson |
Use repository dependency for samtools
draft
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| 2012-12-28 |
Jim Johnson |
Add BQSR and plot_pdf_file options to base_recalibrator.xml
draft
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| 2012-12-28 |
Jim Johnson |
Replace covariate DinucCovariate with ContextCovariate
draft
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| 2012-12-28 |
Jim Johnson |
Remove thread options from base_recalibrator.xml
draft
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| 2012-12-28 |
Jim Johnson |
Fix base_recalibrator.xml option: no_standard_covs
draft
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| 2012-12-28 |
Jim Johnson |
remove thread options from indel_realigner.xml
draft
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| 2012-12-28 |
Jim Johnson |
remove thread options from realigner_target_creator.xml
draft
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| 2012-12-20 |
Jim Johnson |
Update tool_dependencies to GATK v 2.3
draft
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| 2012-11-15 |
Jim Johnson |
Many fixes to haplotype_caller
draft
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| 2012-11-15 |
Jim Johnson |
base_recalibrator out_puts gatk_report
draft
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| 2012-11-15 |
Jim Johnson |
Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2
draft
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| 2012-11-08 |
Jim Johnson |
Remove unneeded params
draft
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| 2012-11-08 |
Jim Johnson |
Fix output filters
draft
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| 2012-11-08 |
Jim Johnson |
Add help to HaplotypeCaller
draft
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| 2012-11-08 |
Jim Johnson |
Add HaplotypeCaller
draft
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| 2012-11-06 |
Jim Johnson |
Comment out site options from reduce_reads.xml
draft
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| 2012-11-06 |
Jim Johnson |
Fix dir path to GenomeAnalysisTKLite.jar
draft
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| 2012-11-06 |
Jim Johnson |
Update tool_dependencies.xml
draft
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| 2012-11-06 |
Jim Johnson |
Cleanup reduce_reads.xml
draft
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| 2012-11-06 |
Jim Johnson |
ReduceReads added
draft
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| 2012-11-02 |
Jim Johnson |
Quote the tool_dependencies.xml GATK2_SITE_OPTIONS action text
draft
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| 2012-11-01 |
Jim Johnson |
tool_dependencies.xml - fix set_environment
draft
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| 2012-11-01 |
Jim Johnson |
tool_dependencies.xml - fix move_file and add symlink
draft
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| 2012-11-01 |
Jim Johnson |
tool_dependencies.xml - fix move_file and add symlink
draft
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| 2012-11-01 |
Jim Johnson |
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
draft
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| 2012-11-01 |
jjohnson |
Uploaded
draft
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