depristo 46cd227613 Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4845 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-15 14:56:12 +00:00
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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
getFirehosePipelineYaml.sh	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
makeResources.sh	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
queueStatus.csh	minor improvements to queue status	2010-10-06 14:34:35 +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
runGATKReport.csh	Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers	2010-12-15 14:56:12 +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
syncWithDevOnGSA2.csh	Useful script for me	2010-11-18 15:21:06 +00:00