In Picard's IlluminaBasecallsToSam and IlluminaBasecallsToFastq, the default setting of
APPLY_EAMSS_FILTER is set to true. We've noticed that newer versions of Illumina's bcl2fastq (version 2) does not perform EAMSS or even allows the user to select EAMSS filtering. Just wondering if in your pipelines you always perform EAMSS filtering regardless of Illumina's sequencing platform model (HiSeq, MiSeq, etc).
Thanks in advance,