gatk-3.8

gatk3的最后一个经典版本3.8

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depristo 20db00a3e8 Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4042 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-16 13:46:22 +00:00
R	plot now assumes 1 / 1000 is the min error rate, not 1/100	2010-08-11 14:48:22 +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	Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.	2010-08-16 13:46:22 +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	Created a new playground script for cleaning bams in Firehose.	2010-08-13 23:52:24 +00:00
perl	no INFO output now that it's the default	2010-08-11 18:56:28 +00:00
python	now support -o output option, useful for pipelines	2010-08-06 14:57:04 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	functional recalibrate script	2010-08-14 16:01:37 +00:00
settings	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
shell	Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am	2010-08-07 12:36:28 +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	Created a new playground script for cleaning bams in Firehose.	2010-08-13 23:52:24 +00:00
ivy.xml	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00