delangel be75b087ec 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. ... b) Add "OG" annotation to genotypes. If Beagle changes genotypes, this annotation gets the original genotype call, to ease performance comparisons. If not, this annotation gets an empty value. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3723 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-06 18:33:28 +00:00
..
TraverseTest.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
TraverseTestProf.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
buildRODs.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
calcCallerMD5s.csh	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
makeResources.sh	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
mergeText.sh	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
readStatsDiff.sh	Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome.	2009-06-02 21:19:39 +00:00
runbeagle.sh	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
splitIntervals.sh	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00