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Is the Knownsites parameter compulsory to be used in BaseRecalibrator ?

deepuedeepue HelsinkiMember
edited April 2015 in Ask the GATK team

Hi,

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.

Thanks

Post edited by deepue on

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