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==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 (stdin is not support as input):
# Build Recalibration Table
# Build Recalibration Table
# Apply Recalibration Table
# Apply Recalibration Table
NOTE: GATK ignores/skips adapters, but our logic does not.
NOTE: GATK ignores/skips adapters, but our logic does not.
== How to use it ==
== How to use it ==
<pre>
<pre>
Required General Parameters :
Required General Parameters :
--in <infile> : input BAM file name
--out <outfile> : output recalibration file name
Optional General Parameters :
Optional 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
Recab Specific Required Parameters
Recab Specific Required Parameters
--refFile <reference file> : reference file name
Recab Specific Optional Parameters :
Recab 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
--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 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.
</pre>
</pre>
{{PhoneHomeParamDesc}}
== Required Generic Parameters ==
== Required Generic Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile|noStdin=1}}
{{outBAMOutputFile}}
{{outBAMOutputFile}}
=== Skip Records with any of the Specified Flags (<code>--buildExcludeFlags</code>, <code>--applyExcludeFlags</code>) ===
=== Skip Records with any of the Specified Flags (<code>--buildExcludeFlags</code>, <code>--applyExcludeFlags</code>) ===
Use <code>--buildExcludeFlags</code> to skip records with any of the specified flags set when building the recalibration table, default 0x704.
Use <code>--buildExcludeFlags</code> to skip records with any of the specified flags set when building the recalibration table, default 0xF04.
By default, when building the recalibration table reads with any of the following flags set are skipped:
By default, when building the recalibration table reads with any of the following flags set are skipped:
* fails QC checks
* fails QC checks
* duplicate
* duplicate
* supplementary alignment
Use <code>--applyExcludeFlags</code> to skip records with any of the specified flags set when applying the recalibration table. The default value is 0x000, do not skip any reads.
Use <code>--applyExcludeFlags</code> to skip records with any of the specified flags set when applying the recalibration table. The default value is 0x000, do not skip any reads.
= Return Value =
= Return Value =
