Geraldine Van der Auwera 175388de1d Merge pull request #396 from broadinstitute/mc_dt_excessive_coverage_defaults ... Updating excessive coverage default parameter & docs+test for QualifyMissingIntervals		2013-09-20 15:12:16 -07:00
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annotator	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00
beagle	Simpler FILTER and info field encoding for BeagleOutputToVCF	2013-06-14 15:56:13 -04:00
bqsr	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00
compression/reducereads	Two reduce reads updates/fixes:	2013-08-01 14:34:59 -04:00
diagnostics	Automated interpretation for QualifyMissingIntervals	2013-09-20 16:47:12 -04:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00
haplotypecaller	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00
indels	Another fix for the Indel Realigner that arises because of secondary alignments.	2013-06-21 16:59:22 -04:00
phasing	Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records.	2013-08-21 15:46:57 -04:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	adding a check for the UNAVAILABLE case of GenotypeType in CountVariants	2013-08-29 17:27:00 -04:00
variantrecalibration	Remove org.apache.commons.collections.IteratorUtils dependency from the test suite	2013-08-21 19:44:02 -04:00
variantutils	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00