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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%
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chartl d5cda76c8b A new subversion repository for matlab scripts, so they don't go away in case of catastrophic Yang failure. 
Might be useful if you want to learn matlab or make use of matlab scripts. It does have some advantages over R (and some disadvantages as well)

This script loads data from the FHS directory listing the average DoC per exon per gene per pool and makes a gene-by-gene box plot of the resulting data, broken up between pilot and production. It will also automatically save the resulting figures if you un-comment two lines.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2181 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-30 16:25:07 +00:00
R R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design. 2009-09-22 18:10:14 +00:00
c Add a Unix-standard version number to the file. 2009-11-23 20:07:17 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP(). 2009-11-30 01:39:01 +00:00
matlab A new subversion repository for matlab scripts, so they don't go away in case of catastrophic Yang failure. 2009-11-30 16:25:07 +00:00
packages Add IlluminaUtil to picard-private.jar 2009-11-25 19:25:21 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python Better support for comparison to truth. Now emits FP rates for each covariate if a truth file is provided. Also now writes out a detailed recal.log file that can be parsed directly into R 2009-11-29 22:20:40 +00:00
scala/src Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 2009-11-02 06:02:41 +00:00
settings Push version number of picard-private-parts 2009-11-25 19:28:57 +00:00
shell Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 2009-09-04 12:39:06 +00:00
testdata GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
build.xml Build aligner as separate jar file. 2009-11-13 22:29:29 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00