Ryan Poplin 6efbcd99f1 HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling.		2012-07-17 14:38:36 -04:00
..
R	Bugfix for R 2.15 not including reshape	2012-06-14 16:42:29 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling.	2012-07-17 14:38:36 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Update the DPP and PBPP to use the BQSRv2 walkers	2012-07-17 13:15:32 -04:00
testdata	Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.	2012-07-04 00:21:21 -04:00