3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
# Build Recalibration Table
# Build Recalibration Table
# Apply Recalibration Table
# Apply Recalibration Table
The Recalibration Table groups bases based on a set of covariates:
The Recalibration Table groups bases based on a set of covariates:
* Read Group
* Read Group
* Quality (either from the quality string or from a tag)
* Quality (either from the quality string or [[#Read the quality from a tag (--qualField)|from a tag]])
* Cycle (reverse complement for reverse strands)
* Cycle (reverse complement for reverse strands)
* 1st/2nd read in pair
* 1st/2nd read in pair
The Recalibration Table tracks the number of matches/mismatches for each set of covariates.
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:
Only bases meeting all of the following criteria are used to Build the Recalibration Table:
* Base criteria
* Base criteria
** match/mismatch (not an insertion/deletion/skip/clip)
** match/mismatch (not an insertion/deletion/skip/clip)
** not a dbSNP position
** not a [[#DBSNP File (--dbsnp)|dbSNP position]]
** base quality > minBaseQual (5 by default)
** base quality > [[#Minimum Recalibration Base Quality (--minBaseQual)|minBaseQual (5 by default)]]
* Additional criteria for cycle != 1 (can be turned off via flags)
* Additional criteria for cycle != 1 (can be turned off via flags)
** previous base is a CIGAR Match/Mismatch
** previous base is a CIGAR Match/Mismatch
** previous base position is not a dbSNP position
** previous base position is not a [[#DBSNP File (--dbsnp)|dbSNP position]]
The Recalibration Table is applied to all bases meeting all of the following criteria (even if they were not used for creating the table):
* base quality > [[#Minimum Recalibration Base Quality (--minBaseQual)|minBaseQual (5 by default)]]
* at least 1 match or mismatch for the set of covariates
Recalibrated Quality is: <math>-10 * \log \frac{mismatches + 1}{mismatches + matches + 1}</math>
If the Recalibrated Quality is greater than [[#Maximum Recalibration Base Quality (--maxBaseQual)|maxBaseQual]], the updated quality is set to maxBaseQual.
Optionally, the previous quality can be [[#Store the original quality (--storeQualTag)|stored in a tag]].
The current recalibration logic was designed for recalibrating ILLUMINA data.
The current recalibration logic was designed for recalibrating ILLUMINA data.
