carneiro 36db9bdcd5 Implemented and tested BWA alignment in the data processing pipeline. ... caveat: Right now bwa only supports one read group, so if the original file had multiple @RG lines, only the first one will be kept. (working on a solution to this) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5931 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-02 23:03:07 +00:00
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QuickCCTest.scala	implementation of the Gatherer class for CountCovariates, which makes it now scatter/gatherable. Kudos to the @Gather annotation Khalid just introduced!	2011-03-31 21:15:21 +00:00
dataProcessing.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
dataProcessingV2.scala	Implemented and tested BWA alignment in the data processing pipeline.	2011-06-02 23:03:07 +00:00
downsampling.scala	Added VQSR to the downsampling script and changed memory limits for the clean script.	2011-05-18 20:07:42 +00:00
justClean.scala	Added VQSR to the downsampling script and changed memory limits for the clean script.	2011-05-18 20:07:42 +00:00
justRecalibrate.scala	just recalibrates now recalibrates one sample, fully, not splitting intervals (naming makes more sense)	2011-05-03 21:42:23 +00:00
justRecalibrateEach.scala	recalibrates a dataset splitting between good and bad regions for comparison (used to be named justRecalibrate)	2011-05-03 21:43:09 +00:00
mendelianViolation.scala	No more default callsets, they're now mandatory arguments.	2011-05-23 21:56:43 +00:00
pbCalling.scala	Renaming ContrastiveRecalibrator --> VariantRecalibrator in preparation for move to core	2011-05-03 18:12:47 +00:00