DataProcessingPipeline and --disable_indel_quals
When I try to run the latest version of the DataProcessingPipeline I get the following error message:
ERROR MESSAGE: GATK Lite does not support all of the features of the full version: base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument
However in the recal case class this option is set to be true:
this.disable_indel_quals = true
Any idea how to solve this? It seams to me this is a bug, but I cannot find the source for the PrintReads class (guessing that its not in the public code), so I can't check it myself.