gatk-3.8

gatk3的最后一个经典版本3.8

Go to file

ebanks 44f3c5639a I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such... We can now emit bzipped VCFs from the GATK. Details: any walker that defines a VCFWriter for its @Output (i.e. pretty much every core walker from UG and on), also has associated with it the -bzip (--bzip_compression) boolean argument. When set, it will emit a VCF that is compressed with bzip2. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4093 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-24 04:14:50 +00:00
R	Changing a name of a column for variantevals output for easier reading by R--let me know if this needs to be updated elsewhere; it's just a space to an underscore.	2010-08-19 19:18:16 +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	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...	2010-08-24 04:14:50 +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	Enabling support for any scala used in QScripts.	2010-08-17 22:05:56 +00:00
perl	Change for Chris: don't depend on other Perl modules.	2010-08-17 22:19:13 +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	Updated firehose clean bam pipeline to pull firehose info and push back firehose clean bam.	2010-08-23 20:38:42 +00:00
settings	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +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	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
ivy.xml	I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...	2010-08-24 04:14:50 +00:00