Eric Banks 85626e7a5d We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.		2011-09-19 12:24:05 -04:00
..
examples	Fixed issue reported by chartl where cloned functions lost tags on @Inputs.	2011-09-16 12:46:07 -04:00
lib	moving the example scala scripts to the qscripts package.	2011-07-01 16:14:59 -04:00
DataProcessingPipeline.scala	Just cleaning up	2011-09-07 13:32:40 -04:00
GATKResourcesBundle.scala	We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.	2011-09-19 12:24:05 -04:00
MethodsDevelopmentCallingPipeline.scala	Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.	2011-09-12 12:17:43 -04:00
PacbioProcessingPipeline.scala	BLASR BAMs and new BWA parameters	2011-08-24 17:04:07 -04:00
StandardVariantEvaluation.scala	new home for the core qscripts	2011-06-30 11:32:06 -04:00