gatk-3.8

gatk3的最后一个经典版本3.8

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chartl db54d63fc7 Hahaha yes, ownage. This now works. BTW, Eric, thanks for forwarding the DepthOfCoverage thread to gsamembers. I'd forgotten about reduce by interval. Mighty helpful in this case! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3906 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-30 04:23:02 +00:00
R	A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object.	2010-07-19 12:38:26 +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	Hahaha yes, ownage. This now works.	2010-07-30 04:23:02 +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	It's probably a good idea to look carefully at what you've done before actually committing	2010-07-23 17:06:54 +00:00
perl	1. Updated tests and added integration test for liftover code.	2010-07-12 17:58:18 +00:00
python	Script to split a provided interval list into contigs. Excesses will be dropped into the last provided file. Works like splitIntervals.sh. This is for Queue.	2010-07-29 16:42:53 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator	2010-07-29 22:04:02 +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