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= Usage =
= Usage =
./bam recab (options) --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--minBaseQual <minBaseQual>] [--maxBaseQual <maxBaseQual>] [--blended <weight>] [--fitModel] [--fast] [--keepPrevDbsnp] [--keepPrevNonAdjacent] [--useLogReg]
./bam recab (options) --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--minBaseQual <minBaseQual>] [--maxBaseQual <maxBaseQual>] [--blended <weight>] [--fitModel] [--fast] [--keepPrevDbsnp] [--keepPrevNonAdjacent] [--useLogReg] [--qualField <tag>] [--storeQualTag <tag>] [--buildExcludeFlags <flag>] [--applyExcludeFlags <flag>]
= Parameters =
= Parameters =
(default is to get it from the Quality field)
(default is to get it from the Quality field)
--storeQualTag <quality tag> : tag to store the previous quality into
--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
--applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set
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</pre>
== Required Generic Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile}}
{{outBAMOutputFile}}
{{outBAMOutputFile}}
== Output log & Summary Statistics FileName (<code>--log</code>) ==
== Optional Generic Parameters ==
=== Output log & Summary Statistics FileName (<code>--log</code>) ===
Output file name for writing logs & summary statistics.
Output file name for writing logs & summary statistics.
If this parameter is not specified, it will write to the output file specified in <code>--out</code> + ".log". Or if the output bam is written to stdout (<code>--out</code> starts with '-'), the logs will be written to stderr. If the filename after --log starts with '-' it will write to stderr.
If this parameter is not specified, it will write to the output file specified in <code>--out</code> + ".log". Or if the output bam is written to stdout (<code>--out</code> starts with '-'), the logs will be written to stderr. If the filename after --log starts with '-' it will write to stderr.
== Turn on Verbose Mode (<code>--verbose</code>) ==
=== Turn on Verbose Mode (<code>--verbose</code>) ===
Turn on verbose logging to get more log messages in the log and to stderr.
Turn on verbose logging to get more log messages in the log and to stderr.
{{paramsParameter}}
{{paramsParameter}}
== Reference File (<code>--refFile</code>) ==
{{PhoneHomeParameters}}
== Required Recalibration Parameters ==
=== Reference File (<code>--refFile</code>) ===
The reference file is a required parameter used for comparing read bases to the reference.
The reference file is a required parameter used for comparing read bases to the reference.
== DBSNP File (<code>--dbsnp</code>) ==
== Optional Recalibration Parameters ==
=== DBSNP File (<code>--dbsnp</code>) ===
The dbsnp file that specifies positions to skip recalibrating. Tab delimited file with the chromosome in the first column and the 1-based position in the 2nd column.
The dbsnp file that specifies positions to skip recalibrating. Tab delimited file with the chromosome in the first column and the 1-based position in the 2nd column.
== Minimum Recalibration Base Quality (<code>--minBaseQual</code>) ==
=== Minimum Recalibration Base Quality (<code>--minBaseQual</code>) ===
When recalibrating reads, only positions with a base quality greater than this minimum phred quality will be recalibrated. If <code>--minBaseQual</code> is not specified, it is defaulted to 5.
When recalibrating reads, only positions with a base quality greater than this minimum phred quality will be recalibrated. If <code>--minBaseQual</code> is not specified, it is defaulted to 5.
The ILLUMINA specs indicate that any quality below 5 can be used as an error indicator so we do not want to recalibrate those.
The ILLUMINA specs indicate that any quality below 5 can be used as an error indicator so we do not want to recalibrate those.
== Maximum Recalibration Base Quality (<code>--maxBaseQual</code>) ==
=== Maximum Recalibration Base Quality (<code>--maxBaseQual</code>) ===
This value sets the maximum phred base quality assigned to a base after recalibrating. Any qualities above this value will be set to this value. It is defaulted to 50.
This value sets the maximum phred base quality assigned to a base after recalibrating. Any qualities above this value will be set to this value. It is defaulted to 50.
== Blended Model Weight (<code>--blended</code>) ==
=== Blended Model Weight (<code>--blended</code>) ===
<span style="color:red">TBD - this parameter is not yet implemented.</span>
<span style="color:red">TBD - this parameter is not yet implemented.</span>
== Fit Model (<code>--fitModel</code>) ==
=== Fit Model (<code>--fitModel</code>) ===
Check if the logistic regression model fits the data.
Check if the logistic regression model fits the data.
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
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>--fast</code>) ==
=== Fast Recalibration (<code>--fast</code>) ===
Use a compact representation of the Recalibration Table that only allows:
Use a compact representation of the Recalibration Table that only allows:
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>]].
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>) ==
=== Allow Previous Base DBSNP (<code>--keepPrevDbsnp</code>) ===
By default bases where the previous base is in DBSNP are excluded from the Recalibration Table.
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.
This option includes these bases in the building of the Recalibration Table.
== Allow Previous Base Non-Match/Mismatch (<code>--keepPrevNonAdjacent</code>) ==
=== 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.
By default bases where the previous base is not a CIGAR Match/Mismatch are excluded from the Recalibration Table.
== Logistic Regression (<code>--useLogReg</code>) ==
=== Logistic Regression (<code>--useLogReg</code>) ===
Use the logistic regression empirical qualities for setting the new base qualities instead of the default formula.
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>]].
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>) ==
=== Read the quality from a tag (<code>--qualField</code>) ===
If this parameter is set, then read the quality string from the specified tag name. If the tag is not found, the quality is read from the quality field.
If this parameter is set, then read the quality string from the specified tag name. If the tag is not found, the quality is read from the quality field.
== Store the original quality (<code>--storeQualTag</code>) ==
=== Store the original quality (<code>--storeQualTag</code>) ===
If this parameter is set, the original quality will be stored as a string in the specified tag.
If this parameter is set, the original quality will be stored as a string in the specified tag.
=== 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.
By default, when building the recalibration table reads with any of the following flags set are skipped:
* unmapped
* secondary alignment
* fails QC checks
* duplicate
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.
These parameters were added in version 1.0.10.
= Return Value =
= Return Value =
Returns -1 if input parameters are invalid.
Returns -1 if input parameters are invalid.
Returns the SamStatus for the reads/writes (0 on success).
Returns the SamStatus for the reads/writes (0 on success, non-0 on failure).
