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gatk3的最后一个经典版本3.8
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Java 95.8%
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delangel e6e8a20a1e 1) Fix MyHaplotypeScore to ignore 454 reads, since all those pathological non-existing indels make some sites' score blow up. If a site is only covered by 454 reads, we (hopefully) detect this graciously and just emit a score of 0.0 for the site. 
2) New annotation SByDepth = log10(-StrandBias/Depth) (non-standard annotation, key name = "SBD"). If StrandBias/Depth happens to be positive (very rare but can happen), annotation gets value=-1000. 
3) Abstracted out new class AnnotationByDepth so that QD and SBD can share code.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3930 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-04 15:23:08 +00:00
R A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object. 2010-07-19 12:38:26 +00:00
archive Archiving 2010-07-27 02:47:18 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java 1) Fix MyHaplotypeScore to ignore 454 reads, since all those pathological non-existing indels make some sites' score blow up. If a site is only covered by 454 reads, we (hopefully) detect this graciously and just emit a score of 0.0 for the site. 2010-08-04 15:23:08 +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 Updated resources package descriptor with dbsnp 129 for b37. 2010-08-03 02:42:48 +00:00
perl 1. Updated tests and added integration test for liftover code. 2010-07-12 17:58:18 +00:00
python Be smart about the headers. 2010-07-30 16:11:16 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator 2010-07-29 22:04:02 +00:00
settings fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no 2010-07-23 18:39:55 +00:00
shell a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype. 2010-07-06 18:33:28 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +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 A Java sizeof, implemented using the Java instrumentation API. Can either get the memory consumed either only by a single 2010-07-27 18:44:15 +00:00
ivy.xml adding the annotations for findbugs as dependencies in the GATK. They have to be in the default config so that we can 2010-07-19 16:34:57 +00:00