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gatk3的最后一个经典版本3.8
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chartl 236764b249 Major (and useful) changes to MultiSampleConcordance: 
1) Now cares about Genotype filtering. If it is flagged as filtered, it can count as a FP/FN/TP; but goes into a "non-confident genotype" bin, rather than het/hom.

2) Can give it a Genotype Confidence flag (-GC) which will automatically filter genotypes in the way above for quality > Q for "-GC Q"

3) Can give it an -assumeRef flag. For sites only in the truth VCF (that don't even appear in the variant VCF), that locus will be treated as confident
   ref calls for all individuals in the variant VCF; and the calculators updated accordingly.

*** Important: Default behavior is that sites unique to the truth VCF are considered no-call sites for the variant. This flag can help get aroudn that;
    however the safest way to run this is to have a variant VCF with calls at each and every locus, if that is possible.

VCFGenotypeRecord -- added an isFiltered() call to automate looking up the FILTERED flag for VCF v3.3

SimpleVCFIntersectWalker - basic outline for a walker I'm working on tonight.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2747 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-30 01:18:31 +00:00
R Added a new option for indicating the mean number of variants on the AnalyzeAnnotations plots. This way one can say, for example, filtering at this point will keep 75 percent of all the variants. 2010-01-29 21:58:31 +00:00
archive Making a copy here before changing the live copy 2010-01-27 20:44:15 +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 Major (and useful) changes to MultiSampleConcordance: 2010-01-30 01:18:31 +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 Give the symlink on the webserver a name that would be a bit more obvious. 2010-01-28 00:40:20 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python Quick script that changes "chr#" to "#" and "chrM" to "MT" and moves mitochondria to the end of the vcf; in accordance with the 1KG reference. 2010-01-28 21:59:33 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +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 New Picard and SAM-JDK with automatic sequence name truncation 2010-01-11 20:49:13 +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 Fully qualify the target for the output file so that external build processes (aka firehose) 2010-01-26 23:06:30 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00