gatk-3.8

gatk3的最后一个经典版本3.8

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depristo 2a803e9044 simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3352 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-12 13:39:09 +00:00
R	Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian.	2010-05-09 16:48:07 +00:00
archive	more clean-up: moving AlleleBalanceInspector to archive.	2010-04-16 20:53:33 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes	2010-05-12 13:36:31 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	adding the Tribble codecs to the package.	2010-05-06 21:06:15 +00:00
perl	Add argument to sortByRef for specifying the tmp directory for sorting.	2010-05-07 13:53:26 +00:00
python	simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36	2010-05-12 13:39:09 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +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	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +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	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Appropriate build statements for 'MarkAllAlignmentsAsPrimary' and 'RepairSeattleBAM' - both one-off tools.	2010-05-10 15:17:51 +00:00
ivy.xml	updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to	2010-05-06 02:08:41 +00:00