gatk-3.8

gatk3的最后一个经典版本3.8

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corin 59495c7f03 Updated tearsheet function utility git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5883 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-26 19:58:57 +00:00
R	Updated tearsheet function utility	2011-05-26 19:58:57 +00:00
analysis/depristo	CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself.	2011-05-21 14:02:30 +00:00
archive	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
chainFiles	Renamed for consistency	2011-05-25 02:12:21 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	OK, this time REALLY fix cut and paste error	2011-05-26 19:47:12 +00:00
lua	Have a list of bam files but Picard updated their versions from v1 to v17 ? This script will update all your v* numbers for you.	2011-05-23 21:46:14 +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	Added cofoja to the Queue package. Although BCEL doesn't think they're needed the scala compiler respectfully disagrees.	2011-05-26 17:42:34 +00:00
perl	Quit immediately with an error message if any of the individual steps fails.	2011-04-22 13:23:33 +00:00
python	A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)	2011-03-21 16:11:55 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Moving the hg19 reference to a new location as per instruction from our intrepid leader	2011-05-25 17:48:59 +00:00
settings	Contracts for Java (http://code.google.com/p/cofoja/) infrastructure enabled. No piece of code actually uses this, so it's possible to remove easily. Does not build by default (you must modify build.xml). Really an intermediate commit so I can play around with the system in my java classes and revert safely. Very much looking forward to DVCS	2011-05-18 18:05:59 +00:00
shell	Useful utility for looking at the file size of GSA file systems	2011-04-02 03:47:27 +00:00
testdata	Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting	2011-05-04 13:56:01 +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	Build for tests now includes path to contracts	2011-05-22 19:44:49 +00:00
ivy.xml	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00