zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk3的最后一个经典版本3.8
2,112 Commits
1 Branch
0 Tags
257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
Go to file
chartl 23983b2fd8 New annotation: ResidualQuality 
Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space.

Update to the integration test so bamboo doesn't look as though someone murdered it with a spork




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-23 20:04:01 +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 BWA: odds and ends. Get rid of some spurious debug code that was accidentally 2009-11-22 15:26:07 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java New annotation: ResidualQuality 2009-11-23 20:04:01 +00:00
packages Picard-private with classes for reading Picard dbSNP binary file 2009-11-19 17:24:28 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python General bug fixes for snpSelector. More robust error checking and handling of NaN values. 2009-11-21 14:48:29 +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 Update xml descriptor with proper version number. 2009-11-19 17:32:22 +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