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Is the Knownsites parameter compulsory to be used in BaseRecalibrator ?
I would like to know about the -knownSites of the BaseRecalibrator. How to get the latest available list for this? How to use this, when we want to identify the unknown variant sites ? What are the steps need to be used instead of the "Quality score recalibration-CountCovariates, TableRecalibration" which were available in the older versions of GATK.