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* Base is a CIGAR Match/Mismatch
* Base is a CIGAR Match/Mismatch
* Previous base is a CIGAR Match/Mismatch or it is the first cycle
* Previous base is a CIGAR Match/Mismatch or it is the first cycle
* Base position is not a dbSNP position
* Previous base position is not a dbSNP position (if not first cycle)
* Base quality > 5 (or the configurable minimum)
The Recalibration Table is applied on all bases in the read sequence (ignoring the alignment/CIGAR). If the base or the pre-base are an 'N', average the 4 alternatives.
The Recalibration Table is applied on all bases in the read sequence (ignoring the alignment/CIGAR) unless the base quality is < 5 (or the configurable minimum)
This recalibration logic was designed for recalibrating ILLUMINA data.
== How to use it ==
== How to use it ==
