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
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examples	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	Updated script to properly bin DoC values so that down-sampling corresponds to range of DoC values obtainable	2011-02-07 16:47:55 +00:00
playground	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00