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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Ryan Poplin 3503050a39 Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller 
-- Adding changes to CombineVariants to work with the Reference Model mode of the HaplotypeCaller.
-- Added -combineAnnotations mode to CombineVariants to merge the info field annotations by taking the median
-- Added new StrandBiasBySample genotype annotation for use in computing strand bias from single sample input vcfs
-- Bug fixes to calcGenotypeLikelihoodsOfRefVsAny, used in isActive() as well as the reference model
-- Added active region trimming capabilities to the reference model mode, not perfect yet, turn off with --dontTrimActiveRegions
-- We only realign reads in the reference model if there are non-reference haplotypes, a big time savings
-- We only realign reads in the reference model if the read is informative for a particular haplotype over another
-- GVCF blocks will now track and output the minimum PLs over the block

-- MD5 changes!
-- HC tests: from bug fixes in calcGenotypeLikelihoodsOfRefVsAny
-- GVCF tests: from HC changes above and adding in active region trimming
 		2013-09-06 16:56:34 -04:00
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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 Update MD5s and the Diagnose Target scala script 2013-05-13 12:06:17 -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