gatk3的最后一个经典版本3.8

depristo d8b8f857f3 V2 -- now working -- of a core walker that creates the standard GATK resource bundle ... See https://www.broadinstitute.org/gsa/wiki/index.php/GATK_resource_bundle Which live locally in /humgen/gsa-hpprojects/GATK/bundle/current You use this following command to create the bundle: java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar dist/Queue.jar -S scala/qscript/core/GATKResourcesBundle.scala --gatkjarfile dist/GenomeAnalysisTK.jar -bsub -jobQueue gsa -svn 5660 $* Annoyingly, it must be run in the trunk directory, and requires an explicit svn version number to create the directory. It also must be run in two stages manually. First, the local bundle is created, and then with the -phase2 argument all of the files in the local bundle are compressed and pushed to the FTP server. I'm likely going to shift most of my processes over to using this location for data file access, especially for b37 data sets. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5665 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-20 12:48:47 +00:00
R	Moved scripts to phasing/scripts sub-directory	2011-04-11 15:25:39 +00:00
analysis/depristo	Scripts for creating S3 IGV account	2011-04-02 13:39:47 +00:00
archive	Moving GLF code to archive	2011-01-15 22:42:42 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
chainFiles	useful chain files	2011-04-18 19:47:49 +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	Simple optimizations for cases where there is no data or RODs at sites, such as with the FastaStats walker. private static immutable Lists and Maps in underlying data structures that have no associated data. Also, avoiding a double map.get() in the low-level genome loc parser. RefMetaDataTracker is now	2011-04-20 10:52:16 +00:00
lua	forgot to remove a debug line.	2011-02-15 16:25:48 +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	Another case of just because you can do something doesn't mean you should.	2011-04-15 15:39:56 +00:00
perl	2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror	2011-02-22 04:17:36 +00:00
python	A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)	2011-03-21 16:11:55 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	V2 -- now working -- of a core walker that creates the standard GATK resource bundle	2011-04-20 12:48:47 +00:00
settings	Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's.	2011-04-01 01:40:41 +00:00
shell	Useful utility for looking at the file size of GSA file systems	2011-04-02 03:47:27 +00:00
testdata	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +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	Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean].	2011-04-08 18:44:32 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00