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gatk3的最后一个经典版本3.8
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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
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller 2013-09-06 16:56:34 -04:00
public Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller 2013-09-06 16:56:34 -04:00
settings - update picard, sam, variants and tribble after fixing bug in BCF2Utils.makeDictionary as reported in ticket 52571227 2013-08-21 12:06:42 -04:00
.gitignore Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
README.md Update README file for the 2.6 release 2013-06-20 13:08:29 -04:00
build.xml build.xml: make ant -p output only important build targets 2013-07-19 14:35:00 -04:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
ivy.xml Brought all of ReduceReads to fastutils 2013-02-23 22:53:23 -05:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/