• Fixed a bug in IlluminaBasecallsToFastq where ADAPTERS_TO_CHECK could not be set as a CLP argument. (#1740)
• Fixed a bug in GtcToVcf where where SOURCE fields populated from the Illumina manifest that contain a semicolon may be incorrectly populated in the INFO field of the VCF (#1738)
• Updated CombineGenotypingArrayVcfs to handle differences in INFO:SOURCE field of a VCF generated by GtcToVcf (#1739)
• Added more logging to IlluminaBaseCallsToSam/Fastq (#1735)