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annotator
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moved SnpEffUtilUnitTest to public tree
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2013-07-30 17:51:40 -04:00 |
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beagle
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Simpler FILTER and info field encoding for BeagleOutputToVCF
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2013-06-14 15:56:13 -04:00 |
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bqsr
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Removed plots generation from the BaseRecalibration software
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2013-06-19 14:47:56 -04:00 |
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compression/reducereads
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Two reduce reads updates/fixes:
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2013-08-01 14:34:59 -04:00 |
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diagnostics
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Update MD5s and the Diagnose Target scala script
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2013-05-13 12:06:17 -04:00 |
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diffengine
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Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)
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2013-03-12 10:57:14 -04:00 |
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fasta
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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filters
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Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).
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2013-04-05 00:52:32 -04:00 |
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genotyper
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Added onlyEmitSamples argument to UnifiedGenotyper
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2013-08-09 11:00:15 -04:00 |
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haplotypecaller
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Bugfix for ReferenceConfidenceModel
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2013-08-06 16:00:32 -04:00 |
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indels
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Another fix for the Indel Realigner that arises because of secondary alignments.
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2013-06-21 16:59:22 -04:00 |
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phasing
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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validation
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MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods
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2013-03-29 14:52:10 -04:00 |
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varianteval
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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variantrecalibration
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Adding mode to VQSR to not output variant records that are filtered out after applying the recalibration. Necessary for 1000G calling.
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2013-08-12 11:22:59 -04:00 |
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variantutils
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CombineVariants no longer adds PASS to unfiltered records
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2013-05-20 16:53:51 -04:00 |
a45011d7e7