gatk-3.8

gatk3的最后一个经典版本3.8

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ebanks 2a5349d886 VariantAnnotator now adds dbsnp id if a dbsnp rod is supplied and it's not already set for a record git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2100 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-20 03:26:09 +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	Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still	2009-11-19 21:20:03 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	VariantAnnotator now adds dbsnp id if a dbsnp rod is supplied and it's not already set for a record	2009-11-20 03:26:09 +00:00
packages	Picard-private with classes for reading Picard dbSNP binary file	2009-11-19 17:24:28 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	cleanup of SNP selector -- ready for some additional testing	2009-11-13 21:46:31 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	Update xml descriptor with proper version number.	2009-11-19 17:32:22 +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	Build aligner as separate jar file.	2009-11-13 22:29:29 +00:00
ivy.xml	Extract and include only the Tim Fennell-approved parts of picard private.	2009-11-13 19:42:33 +00:00