Ryan Poplin bf2d5efe4d Moving HaplotypeCaller integration and unit tests over to protected as well.		2012-07-17 14:51:26 -04:00
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bqsr	1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method.	2012-07-17 12:23:40 -04:00
compression/reducereads	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
haplotypecaller	Moving HaplotypeCaller integration and unit tests over to protected as well.	2012-07-17 14:51:26 -04:00