gatk-3.8

gatk3的最后一个经典版本3.8

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depristo e0abb73fd7 plot now assumes 1 / 1000 is the min error rate, not 1/100 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4010 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-11 14:48:22 +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	Added option to print out discordant sites in GenotypeConcordance	2010-08-10 19:55:19 +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	A quickly hacked together replacement for AnnotateVCFwithMAF.py, which doesn't work anymore with Cancer's updated annotator. Takes an annotated MAF file and imports the annotations into the VCF file. For the MAF annotator's DNP and TNP annotations (which I think are likely to not be correct, given the lack of phasing information or even proper association to the same sample), just propagate the annotation from the previous annotated variant to which the multinucleotide polymorphism was associated.	2010-08-11 00:20:08 +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	full path to Rscript	2010-08-10 12:02:38 +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	Fixed a problem when mixing queue with other targets, such as 'ant clean oneoffs queue' and the STING_BUILD_TYPE environment is set.	2010-08-09 17:59:51 +00:00
ivy.xml	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00