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= Overview of the <code>recab</code> function of <code>[[bamUtil]]</code> =
= Overview of the <code>recab</code> function of <code>[[bamUtil]]</code> =
The <code>recab</code> option of [[bamUtil]] recalibrates a SAM/BAM file.
The <code>recab</code> option of [[bamUtil]] recalibrates a SAM/BAM file.
Recalibration can also be called as an option of [[bamUtil: dedup]]. This will perform the recalibration and the deduping in the same set of steps, increasing processing speed.
==Handling Recalibration/Implementation Notes==
==Handling Recalibration/Implementation Notes==
Recalibration is a 2-step process that loops through the file twice:
Recalibration is a 2-step process that loops through the file twice:
# Apply Recalibration Table
# Apply Recalibration Table
Recalibration is done by grouping bases based on a set of covariates:
The Recalibration Table groups bases based on a set of covariates:
* Read Group
* Read Group
* Cycle
* Quality (either from the quality string or from a tag)
* Cycle (reverse complement for reverse strands)
* 1st/2nd read in pair
* 1st/2nd read in pair
* Previous Cycle's Base
* Previous Cycle's Base (reverse complement for reverse strands)
* This Cycle's Base
* This Cycle's Base (reverse complement for reverse strands)
The Recalibration Table tracks the number of matches/mismatches for each set of covariates.
Only bases meeting all of the following criteria are used to Build the Recalibration Table:
* Read criteria
** not a duplicate
** mapped
** mapping quality != 0
** mapping quality != 255
* Base criteria
** match/mismatch (not an insertion/deletion/skip/clip)
** not a dbSNP position
** base quality > minBaseQual (5 by default)
* Additional criteria for cycle != 1 (can be turned off via flags)
** previous base is a CIGAR Match/Mismatch
** previous base position is not a dbSNP position
The Recalibration Table is applied to all bases meeting all of the following criteria:
* base quality > minBaseQual (5 by default)
The Recalibrated Quality is calculated using: <math>-10 * \log \frac{mismatches + 1}{mismatches + matches + 1}</math>
If the Recalibration Table has no matches & no mismatches for a set of covariates, the original base quality is kept.
If the Recalibrated Quality is greater than maxBaseQual, the updated quality is set to maxBaseQual.
Optionally, the previous quality can be stored in a tag.
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)
The current recalibration logic was designed for recalibrating ILLUMINA data.
== How to use it ==
== How to use it ==
