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Does the tool BaseRecalibrator use only variants that have passed all filtration steps?
BaseRecalibrator tools requires known sites which I don't have so I have read that one can iteratively call variants and use the set that passes the hard filtering cutoffs as input for the recalibration.
So, after hard filtering, I have variants that passed and did not pass in the vcf file - do I need to write the ones that passed to a separate file that is fed into the recalibration or can I just feed in all - so does the tool BaseRecalibrator use only variants that have passed all filtration steps?