chartl 21ec44339d Somewhat major update. Changes: ... - ProduceBeagleInputWalker + Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present + Takes a bootstrap argument -- can use some given %age of the validation sites + Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap -BeagleOutputToVCFWalker + Now filters sites where the genotypes have been reverted to hom ref + Now calls in to the new VCUtils to calculate AC/AN -Queue + New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype + full calling pipeline v2 uses the above libraries + minor changes to some of my own scripts + no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-08 13:30:28 +00:00
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chartl	Somewhat major update. Changes:	2010-10-08 13:30:28 +00:00
depristo	More Queue scripts for analysis	2010-09-12 14:04:10 +00:00
examples	Fixed VariantEval rod binding names.	2010-09-24 14:52:51 +00:00
kshakir	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
rpoplin	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
fullCallingPipeline.q	upping mem limit since something was unhappy with the lower limit	2010-10-05 02:38:17 +00:00
recalibrate.scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00