Changes

Reads Not Recalibrated:* Duplicates* Unmapped* Mapping Quality = 0* Mapping Quality = 255 Recalibration is a 2-step process that loops through the file twice(stdin is not support as input):

 The Recalibration is done by grouping Table groups bases based on a set of covariates:

* Quality (either from the quality string or [[#Read the quality from a tag (--qualField)|from a tag]])* Cycle(reverse complement for reverse strands)

* Previous Cycle's Base(reverse complement for reverse strands)* 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 File (--dbsnp)|dbSNP position]]** base quality > [[#Minimum Recalibration Base Quality (--minBaseQual)|minBaseQual (5 by default)]]* Additional criteria for cycle != 1 (can be turned off via flags)** previous base is a CIGAR Match/Mismatch (Use [[#Allow Previous Base Non-Match/Mismatch (--keepPrevNonAdjacent)|<code>--keepPrevNonAdjacent</code>]] to disable)** previous base position is not a [[#DBSNP File (--dbsnp)|dbSNP position]] (Use [[#Allow Previous Base DBSNP (--keepPrevDbsnp)|<code>--keepPrevDbsnp</code>]] to disable)  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> Alternatively, [[#Logistic Regression (--useLogReg)|logistic regression]] can be used for calculating the new quality. If the Recalibrated Quality is greater than [[#Maximum Recalibration Base Quality (--maxBaseQual)|maxBaseQual]], the updated quality is set to maxBaseQual.

Not all bases are used for building Optionally, 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 previous quality can be [[#Store the first cycle* Base position is not a dbSNP position* Previous base position is not a dbSNP position (if not first cycle)* Base original quality > 5 (or the configurable minimum--storeQualTag)|stored in a tag]].

This The current recalibration logic was designed for recalibrating ILLUMINA data. NOTE: GATK ignores/skips adapters, but our logic does not.

./bam recab (options) --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--minBaseQual <minBaseQual>] [--maxBaseQual <maxBaseQual>] [--blended <weight>] [--recabLogRegfitModel] [--fast] [--keepPrevDbsnp] [--keepPrevNonAdjacent] [--useLogReg] [--qualField <tag>] [--storeQualTag <tag>] [--buildExcludeFlags <flag>] [--applyExcludeFlags <flag>]

--in <infile> : input BAM file name --out <outfile> : output recalibration file nameOptional General Parameters : --log <logfile> : log and summary statistics (default: [outfile].log) --verbose : Turn on verbose mode --noeof : do not expect an EOF block on a bam file. --params : print the parameter settings

--refFile <reference file> : reference file nameRecab Specific Optional Parameters : --dbsnp <known variance file> : dbsnp file of positions --minBaseQual <minBaseQual> : minimum base quality of bases to recalibrate (default: 5) --maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50) qualities over this value will be set to this value. This setting is applied after binning (if applicable). --blended <weight> : blended model weight --fitModel : check if the logistic regression model fits the data overriden by fast, but automatically applied by useLogReg --recabLogReg fast : use a compact representation that only allows: * at most 256 Read Groups * maximum quality 63 * at most 127 cycles overrides fitModel, but is overridden by useLogReg uses up to about 2.25G more memory than running without --fast. --keepPrevDbsnp : do not exclude entries where the previous base is in dbsnp when building the recalibration table By default they are excluded from the table. --keepPrevNonAdjacent : do not exclude entries where the previous base is not adjacent (not a Cigar M/X/=) when building the recalibration table By default they are excluded from the table (except the first cycle). --useLogReg : use logistic regression calculated quality for calculating the new quality automatically applies fitModel and overrides fast. --qualField <quality tag> : tag to get the starting base quality (default is to get it from the Quality field) --storeQualTag <quality tag> : tag to store the previous quality into --buildExcludeFlags <flag> : exclude reads with any of these flags set when building the recalibration table. Default is 0xF04 --applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set Quality Binning Parameters (optional): Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used) Ranges are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70 The first bin always starts at 0, so does not need to be specified. By default, the bin value is the low end of the range. --binQualS : Bin the Qualities as specified (phred): minQualOfBin2, minQualofBin3... --binQualF : Bin the Qualities based on the specified file --binMid : Use the mid point of the quality bin range for the quality value of the bin. --binHigh : Use the high end of the quality bin range for the quality value of the bin. 

== Required Generic Parameters =={{inBAMInputFile|noStdin=1}}

== Optional Generic Parameters ===== Output log & Summary Statistics FileName (<code>--log</code>) ===

=== Turn on Verbose Mode (<code>--verbose</code>) ===

== Blended Model Weight = DBSNP File (<code>--blendeddbsnp</code>) ===

<span style="color:red">TBD The dbsnp file that specifies positions to skip recalibrating. Tab delimited file with the chromosome in the first column and the 1- this parameter is not yet implementedbased position in the 2nd column.</span>

=== Minimum Recalibration Base Quality (<code>--minBaseQual</code>) ===

=== Maximum Recalibration Base Quality (<code>--maxBaseQual</code>) ===

== = Blended Model Weight (<code>--blended</code>) === <span style="color:red">TBD - this parameter is not yet implemented.</span> === Fit Model (<code>--fitModel</code>) === Check if the logistic regression model fits the data. This option does NOT set the new qualities to the logistic regression calculated qualities, it only checks the fit. To apply the logistic regression qualities, see [[#Logistic Regression (--useLogReg)|<code>--useLogReg</code>]]. <code>--fitModel</code> is automatically applied when <code>--useLogReg</code> is specified. This option cannot be used in conjunction with [[#Fast Recalibration (--fast)|<code>--fast</code>]] and is overriden by <code>--fast</code>, but automatically applied by useLogReg == = Fast Recalibration (<code>--recabLogRegfast</code>) === Use a compact representation of the Recalibration Table that only allows:* at most 256 Read Groups* maximum quality 63* at most 127 cycles This option will run faster than the default recalibration, but uses up to about 2.25G more memory than running without --fast. This option cannot be used in conjunction with [[#Fit Model (--fitModel)|<code>--fitModel</code>]], or [[#Logistic Regression (--useLogReg)|<code>--useLogReg</code>]] and overrides [[#Fit Model (--fitModel)|<code>--fitModel</code>]], but is overridden by [[#Logistic Regression (--useLogReg)|<code>--useLogReg</code>]]. === Allow Previous Base DBSNP (<code>--keepPrevDbsnp</code>) === By default bases where the previous base is in DBSNP are excluded from the Recalibration Table. This option includes these bases in the building of the Recalibration Table. === Allow Previous Base Non-Match/Mismatch (<code>--keepPrevNonAdjacent</code>) === By default bases where the previous base is not a CIGAR Match/Mismatch are excluded from the Recalibration Table.

Use This option includes these bases in the logistic regression empirical qualities for setting the new base qualities instead building of the default formula: -10 * log10((#mismatches+1)/(#total+1))Recalibration Table.

 === Logistic Regression (<code>--useLogReg</code>) === Use the logistic regression empirical qualities for setting the new base qualities instead of the default formula. This option automatically enables [[#Fit Model (--fitModel)|<code>--fitModel</code>]] and disables [[#Fast Recalibration (--fast)|<code>--fast</code>]]. === Read the quality from a tag (<code>--qualField</code>) ===

=== Store the original quality (<code>--storeQualTag</code>) ===

Returns the SamStatus for the reads/writes (0 on success, non-0 on failure).