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