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Automatic read filters GATK v3.3.0
Dear GATK team,
Is there a way to find out which automatic read filters were applied in previous GATK version (namely v3.3.0)?
As reported in the current documentation, BadCigarFilter is automatically applied in version 3.5 for RealignerTargetCreator, IndelRealigner, BaseRecalibrator and PrintReads. I'm wondering if it was the case with version 3.3.0 or if I need to specify the option -rf BadCigarFilter with oldest version of gatk?
Thanks a lot!
All the best