kshakir 8040998c15 Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp. ... Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod. Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info). Renamed fCP.q to FCP.q. Though it's still disabled until VariantEval is updated, added changes above to the FCPTest. Removed refseq table from the queue.sh wrapper script. Only specified in the yaml. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-07 22:01:09 +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
getFirehosePipelineYaml.sh	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00
pipelineJobs.csh	watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress	2011-01-09 13:09:30 +00:00
queue.sh	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00
queueStatus.csh	Better queue status messages	2010-12-22 20:17:28 +00:00
runGATKReport.csh	Missed one uncomment	2011-02-01 13:01:59 +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	V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism	2011-01-24 16:45:07 +00:00