Valentin Ruano-Rubio 08f92bb6f9 Added AnalyzeCovariates tool to generate BQSR assessment quality plots. ... Implemtation details: * Added tool class *.AnalyzeCovariates * Added convenient addAll method to Utils to be able to add elements of an array. * Added parameter comparison methods to RecalibrationArgumentCollection class in order to verify that multiple imput recalibration report are compatible and comparable. * Modified the BQSR.R script to handle up to 3 different recalibration tables (-BQSR, -before and -after) and removed some irrelevant arguments (or argument values) from the output. * Added an integration test class.		2013-06-19 14:38:02 -04:00
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gatk/walkers/variantrecalibration	Updating VQSR docs. Removing references to old best practices pages.	2012-08-01 14:30:24 -04:00
queue/util	Improve queue script jobreport visualization script	2013-05-07 12:11:46 -04:00
utils/recalibration	Added AnalyzeCovariates tool to generate BQSR assessment quality plots.	2013-06-19 14:38:02 -04:00