gatk3的最后一个经典版本3.8

rpoplin 5d39cd5db8 Added --fdr_filter_level to ApplyVariantCuts so that you can create beautiful tranche plots and also decide which tranche level to filter at. The previous version always filtered at the smallest tranche. The tranche filter names are appropriately added to the VCF header. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3747 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-08 22:44:10 +00:00
R	useful routines for R	2010-06-30 16:38:49 +00:00
archive	Retiring multi-sample genotyper	2010-05-20 14:11:11 +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 --fdr_filter_level to ApplyVariantCuts so that you can create beautiful tranche plots and also decide which tranche level to filter at. The previous version always filtered at the smallest tranche. The tranche filter names are appropriately added to the VCF header.	2010-07-08 22:44:10 +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	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
perl	Updated for CentOS changes.	2010-07-08 14:36:24 +00:00
python	misc. useful updates to python library	2010-06-30 16:33:32 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Workaround for scala trait erasing parameterized types:	2010-07-07 03:15:10 +00:00
settings	Rev Picard with new IndexedFastaSequenceFile patch.	2010-07-01 03:05:43 +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	adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running.	2010-07-08 19:10:19 +00:00
ivy.xml	adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running.	2010-07-08 19:10:19 +00:00