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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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hanna f275be6968 A 'fat shard' finder. Cranks through the indices of a BAM file or list of 
BAM files looking for outliers (outliers right now are defined naively  as 
shards whose sizes are more than 5 stddevs away from the mean).  Runs in
13 minutes per chromosome on 707 low pass whole genome BAMs -- not great, but
much faster than running UG on the same region to discover anomalies.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5782 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-05-10 12:56:47 +00:00
R Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot. 2011-05-05 20:24:06 +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 Adding chain files for Mark. Tested by lifting over back and forth between builds. Note that they comprise only the standard contigs so no _randoms or GL000xxx.1s. 2011-04-22 14:53:15 +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 A 'fat shard' finder. Cranks through the indices of a BAM file or list of 2011-05-10 12:56:47 +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 Added JavaMail dependencies to Queue package since bcel wasn't picking them up. 2011-04-23 20:48:40 +00:00
perl Quit immediately with an error message if any of the individual steps fails. 2011-04-22 13:23:33 +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 Implemented broad specific LSF requirement in the LSF job runner ahead of GridEngine check in by dheiman. 2011-05-09 22:14:04 +00:00
settings Factor out all testing dependencies into a separate test configuration and 2011-05-05 22:42:11 +00:00
shell Useful utility for looking at the file size of GSA file systems 2011-04-02 03:47:27 +00:00
testdata Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting 2011-05-04 13:56:01 +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 Factor out all testing dependencies into a separate test configuration and 2011-05-05 22:42:11 +00:00
ivy.xml Factor out all testing dependencies into a separate test configuration and 2011-05-05 22:42:11 +00:00