gatk3的最后一个经典版本3.8

hanna b95165e39c Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-01 00:33:18 +00:00
R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00
c	Created walkers for alignment, validation.	2009-10-30 15:04:07 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.	2009-11-01 00:33:18 +00:00
packages	added IndelGenotyperV2Walker	2009-10-29 20:07:31 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Now looks up and propagates Syzygy's LOD scores into the appropriate field (so variantfiltration can adjust lod scores accurately)	2009-10-30 21:13:03 +00:00
scala/src	Major code refactoring:	2009-10-20 14:58:04 +00:00
settings	Bumping version of Picard for firehose compatibility.	2009-10-16 19:38:56 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.	2009-11-01 00:33:18 +00:00
ivy.xml	Delete duplicate jgrapht reference.	2009-10-29 17:38:01 +00:00