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The <code>recab</code> option of [[bamUtil]] recalibrates a SAM/BAM file.
The <code>recab</code> option of [[bamUtil]] recalibrates a SAM/BAM file.
==Handling Recalibration==
==Handling Recalibration/Implementation Notes==
Reads Not Recalibrated:
Reads Not Recalibrated:
* Mapping Quality = 255
* Mapping Quality = 255
Recalibration is a 2-step process that loops through the file twice:
# Build Recalibration Table
# Apply Recalibration Table
Recalibration is done by grouping bases based on a set of covariates:
Recalibration is done by grouping bases based on a set of covariates:
For Reverse Strands, the reverse complement of the SAM/BAM is used for the cycle, previous cycle's base, and current 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.
Not all bases are used for building the Recalibration table. Only bases meeting the following criteria are used:
* Base is a CIGAR Match/Mismatch
* Previous base is a CIGAR Match/Mismatch or it is the first cycle
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.
