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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net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00