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gatk3的最后一个经典版本3.8
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chartl 59416ae06a This is an annotation adapted from one that Mark Daly suggested some time ago. Right now it calculates: 
- For all reference bases, the proportion of their second best bases that support the SNP

- the proportion of non-reference bases that support the SNP

and reports the difference between the two. Initially I was taking depth into account as well, but that did not appear to work as nicely as I'd like (even at 20,000x depth, if 95% of the non-reference bases are C, and 98% of the reference second-best-bases are C, then we would want to be suspicious of it; but perhaps slightly less so than if the depth were only 20...)

Anyway it's now available. I'm not sure how useful it will be, but I spawned the FHS annotation jobs again, so we'll see.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2109 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-22 00:47:49 +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 Refactoring. Push the revisions to the common aligner interface down into 2009-11-20 17:08:09 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java This is an annotation adapted from one that Mark Daly suggested some time ago. Right now it calculates: 2009-11-22 00:47:49 +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