gatk-3.8

gatk3的最后一个经典版本3.8

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kshakir 69f5f16711 Added conditional checking for median_insert_size. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6029 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-22 17:59:54 +00:00
R	Removed nDeletions and nInsertions as independent plots -- just not useful given nIndels and insertions/deletion ratio. Fixed jitter problems with rug plots by removing the rugs entirely. Recovered, and improved, comparative features lost by removing the rug plots by getting viewports to work (trivial) so now per sample metrics and distributions are displayed on the same page!	2011-06-22 13:59:46 +00:00
analysis/depristo	Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files.	2011-06-16 12:56:04 +00:00
archive	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00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	Renamed for consistency	2011-05-25 02:12:21 +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	Removing unnecessary String.format calls	2011-06-22 15:30:52 +00:00
lua	cleaned up the scripts and created an interval library to facilitate future reuse.	2011-05-27 19:35:36 +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	Oops. Failed to add DbSnpMatchMetrics to Picard private jar.	2011-06-14 15:14:19 +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	Added conditional checking for median_insert_size.	2011-06-22 17:59:54 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF	2011-06-19 03:11:00 +00:00
settings	Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script	2011-06-14 17:43:43 +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	Fix for CoFoJa exception by upgrading to latest version	2011-06-09 17:49:15 +00:00
ivy.xml	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00