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Geraldine Van der Auwera 4d20c71e09 Improvements to various gatkdocs 
- Make -rod required
    - Document that contaminationFile is currently not functional with HC
    - Document liftover process more clearly
    - Document VariantEval combinations of ST and VE that are incompatible
    - Added a caveat about using MVLR from HC and UG.
    - Added caveat about not using -mte with -nt
    - Clarified masking options
    - Fixed docs based on Erics comments
 		2013-08-10 10:01:31 -07:00
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java Improvements to various gatkdocs 2013-08-10 10:01:31 -07:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest 2013-02-27 04:45:53 -05:00