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=== Covariates Notes ===
=== Covariates Notes ===
Recalibration is done by grouping bases based on a set of covariates:
* Read Group
* Cycle
* 1st/2nd read in pair
* Previous Cycle's Base
* This Cycle's Base
For Reverse Strands, the reverse complement of the SAM/BAM is used for the cycle, previous cycle's base, and current cycle's base.
== How to use it ==
== How to use it ==
