Geraldine Van der Auwera 1cf66addaa Deprecate tools that were outdated or redundant ... ReadAdaptorTrimmer (unsound and untested) BaseCoverageDistribution (redundant with DiagnoseTargets) CoveredByNSamplesSites (redundant with DiagnoseTargets) FindCoveredIntervals (redundant with DiagnoseTargets) VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests) LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106) (use Picard liftover tool) sortByRef.pl (use Picard SortVCF) ListAnnotations (useless) Also deleted the java archive from the private repository (old junk we never use)		2015-11-20 22:49:40 -05:00
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java/org/broadinstitute/gatk	Deprecate tools that were outdated or redundant	2015-11-20 22:49:40 -05:00
resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration	Logit transform to MQ + jitter MQ capped improves VQSR	2015-08-20 17:53:01 -04:00