rpoplin 00453919d2 VQSR now only uses the valid polymorphic sites for training and truth sensitivity calculations. Any number of tracks whose ROD binding begins with the name truth can be used as truth sensitivity tracks. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5012 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-18 20:48:19 +00:00
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BamProcessing.scala	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +00:00
PipelineArgumentCollection.scala	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
ProjectManagement.scala	PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).	2010-12-22 15:16:15 +00:00
QPipeline.scala	Somewhat major update. Changes:	2010-10-08 13:30:28 +00:00
VariantCalling.scala	VQSR now only uses the valid polymorphic sites for training and truth sensitivity calculations. Any number of tracks whose ROD binding begins with the name truth can be used as truth sensitivity tracks.	2011-01-18 20:48:19 +00:00