gatk-3.8

gatk3的最后一个经典版本3.8

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rpoplin a8d37da10b Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3952 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-05 14:12:19 +00:00
R	Can now set the maximum number of variants to see in a cluster plot (useful when you don't need to see a billion points to get an idea of what's going on. Limit applies to known and novel variants separately.	2010-08-04 18:45:24 +00:00
archive	Archiving	2010-07-27 02:47:18 +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	Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites	2010-08-05 14:12:19 +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	Updated resources package descriptor with dbsnp 129 for b37.	2010-08-03 02:42:48 +00:00
perl	1. Updated tests and added integration test for liftover code.	2010-07-12 17:58:18 +00:00
python	Be smart about the headers.	2010-07-30 16:11:16 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long.	2010-08-04 20:05:27 +00:00
settings	fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no	2010-07-23 18:39:55 +00:00
shell	a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.	2010-07-06 18:33:28 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +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	A Java sizeof, implemented using the Java instrumentation API. Can either get the memory consumed either only by a single	2010-07-27 18:44:15 +00:00
ivy.xml	adding the annotations for findbugs as dependencies in the GATK. They have to be in the default config so that we can	2010-07-19 16:34:57 +00:00