DataProcessingPipeline and --disable_indel_quals
Posted in Ask the GATK team | Last updated on 2012-07-31 15:13:03

Comments (7)

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.

Regards, Johan

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