gatk3的最后一个经典版本3.8

andrewk 845488ff94 VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1347 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-30 21:54:06 +00:00
R	Updated python files	2009-07-07 14:15:39 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls.	2009-07-30 21:54:06 +00:00
packages	Added indel cleaner and quality scores recalibrator to the GATK package.	2009-07-24 16:20:38 +00:00
perl	sortByRef now supports x:y location syntax	2009-07-07 16:42:40 +00:00
python	Skip compiled python files (*.pyc) in svn status output	2009-07-30 21:45:23 +00:00
settings	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00
shell	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
testdata	Derive examples from real data.	2009-07-10 04:21:37 +00:00
build.xml	Exclude secondary base caller code from playground jar. Still TODO: figure	2009-07-30 21:02:46 +00:00
ivy.xml	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00