zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/protected/java/test/org/broadinstitute/sting/utils
History
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
..
genotyper Relaxing the constraints on the readIsPoorlyModelled function. 2013-06-13 11:06:23 -04:00
gvcf Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller 2013-09-06 16:56:34 -04:00
haplotype Better caching for the HaplotypeCaller 2013-08-02 01:27:29 -04:00
haplotypeBAMWriter Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences 2013-07-02 15:46:38 -04:00
nanoScheduler A whole slew of improvements to the Haplotype Caller and related code. 2013-07-12 10:09:10 -04:00
pairhmm Removed native method call 2013-07-30 13:59:58 -04:00
recalibration Added hidden mode for BQSR to force all read groups to be the same one. 2013-05-06 19:09:10 -04:00
smithwaterman New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 2013-05-13 09:36:39 -04:00
ContigComparatorUnitTest.java Generalize and fixup ContigComparator 2013-02-09 09:52:13 -05:00