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[[Category:BamUtil|validate]]
[[Category:BAM Software]]
[[Category:Software]]
='''COMING SOON, June, 2012'''=
= Overview of the <code>recab</code> function of <code>[[bamUtil]]</code> =
The <code>recab</code> option of [[bamUtil]] recalibrates a SAM/BAM file.
==Handling Recalibration==
Reads Not Recalibrated:
* Duplicates
* Unmapped
* Mapping Quality = 0
* Mapping Quality = 255
=== Covariates Notes ===
Duplicates are determined by checking for matching keys.
The Key is comprised of:
# Chromosome
# Orientation (forward/reverse)
# Unclipped Start(forward)/End(reverse)
# Library
Rules:
* Skip Unmapped Reads, they are not marked as duplicate
* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:
*# A paired-end record has the same key (even if the pair is not proper/the mate is unmapped/the mate is not found)<br/>-OR-
*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record)
* Mark both Paired-End Reads Duplicate if:
# Another paired-end pair has the same set of keys and has a higher base quality sum.
This code assumes that at most 1000 bases are clipped at the start of a read.
== How to use it ==
When <code>dedup</code> is invoked without any arguments the usage information is displayed as described below under [[#Usage|Usage]].
The input SAM/BAM file is required, [[#input File (--in)|input File (--in)]], and must be sorted by coordinate.
The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
= Usage =
./bam recab --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--blended <weight>]
= Parameters =
<pre>
Required General Parameters :
--in <infile> : input BAM file name
--out <outfile> : output recalibration file name
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
--refFile <reference file> : reference file name
Recab Specific Optional Parameters :
--dbsnp <known variance file> : dbsnp file of positions
--blended <weight> : blended model weight
</pre>
{{inBAMInputFile}}
{{outBAMOutputFile}}
== BAM File Is Sorted By Read Name (<code>--minRecabQual</code>) ==
When recalibrating reads, only positions with a base quality greater than this minimum will be recalibrated. If <code>--minQual</code> is not specified, it is defaulted to <span style="color:red">TBD</span>.
== Output log & Summary Statistics FileName (<code>--log</code>) ==
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.
== Treat Reads with Mates On Different Chromosomes As Single-Ended (<code>--oneChrom</code>) ==
If a read's mate is not found it will not be used for duplicate marking. If you are running on a single chromosome, all read's whose mates are on different chromosomes will not be used for duplicate marking. The <code>--oneChrom</code> option will treat reads with mates on a different chromosome as single-ended.
== Recalibrate (<code>--recab</code>) ==
This option will recalibrate the input file in addition to deduping.
== Remove Duplicates (<code>--rmDups</code>) ==
Instead of marking a read as duplicate in the flag, the <code>--rmDups</code> option will remove it from the output BAM file.
== Ignore Previous Duplicate Marking (<code>--force</code>) ==
By default the deduper will throw an error and stop if a read is already marked as duplicate. The <code>--force</code> option will removes any previous duplicate marking and marks the reads from scratch. The resulting output file will only have reads determined by the deduper marked as duplicates.
== Turn on Verbose Mode (<code>--verbose</code>) ==
Turn on verbose logging to get more log messages in the log and to stderr.
{{noeofBGZFParameter}}
{{paramsParameter}}
= Return Value =
Returns -1 if input parameters are invalid.
Returns the SamStatus for the reads/writes (0 on success).
[[Category:BAM Software]]
[[Category:Software]]
='''COMING SOON, June, 2012'''=
= Overview of the <code>recab</code> function of <code>[[bamUtil]]</code> =
The <code>recab</code> option of [[bamUtil]] recalibrates a SAM/BAM file.
==Handling Recalibration==
Reads Not Recalibrated:
* Duplicates
* Unmapped
* Mapping Quality = 0
* Mapping Quality = 255
=== Covariates Notes ===
Duplicates are determined by checking for matching keys.
The Key is comprised of:
# Chromosome
# Orientation (forward/reverse)
# Unclipped Start(forward)/End(reverse)
# Library
Rules:
* Skip Unmapped Reads, they are not marked as duplicate
* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:
*# A paired-end record has the same key (even if the pair is not proper/the mate is unmapped/the mate is not found)<br/>-OR-
*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record)
* Mark both Paired-End Reads Duplicate if:
# Another paired-end pair has the same set of keys and has a higher base quality sum.
This code assumes that at most 1000 bases are clipped at the start of a read.
== How to use it ==
When <code>dedup</code> is invoked without any arguments the usage information is displayed as described below under [[#Usage|Usage]].
The input SAM/BAM file is required, [[#input File (--in)|input File (--in)]], and must be sorted by coordinate.
The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
= Usage =
./bam recab --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--blended <weight>]
= Parameters =
<pre>
Required General Parameters :
--in <infile> : input BAM file name
--out <outfile> : output recalibration file name
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
--refFile <reference file> : reference file name
Recab Specific Optional Parameters :
--dbsnp <known variance file> : dbsnp file of positions
--blended <weight> : blended model weight
</pre>
{{inBAMInputFile}}
{{outBAMOutputFile}}
== BAM File Is Sorted By Read Name (<code>--minRecabQual</code>) ==
When recalibrating reads, only positions with a base quality greater than this minimum will be recalibrated. If <code>--minQual</code> is not specified, it is defaulted to <span style="color:red">TBD</span>.
== Output log & Summary Statistics FileName (<code>--log</code>) ==
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.
== Treat Reads with Mates On Different Chromosomes As Single-Ended (<code>--oneChrom</code>) ==
If a read's mate is not found it will not be used for duplicate marking. If you are running on a single chromosome, all read's whose mates are on different chromosomes will not be used for duplicate marking. The <code>--oneChrom</code> option will treat reads with mates on a different chromosome as single-ended.
== Recalibrate (<code>--recab</code>) ==
This option will recalibrate the input file in addition to deduping.
== Remove Duplicates (<code>--rmDups</code>) ==
Instead of marking a read as duplicate in the flag, the <code>--rmDups</code> option will remove it from the output BAM file.
== Ignore Previous Duplicate Marking (<code>--force</code>) ==
By default the deduper will throw an error and stop if a read is already marked as duplicate. The <code>--force</code> option will removes any previous duplicate marking and marks the reads from scratch. The resulting output file will only have reads determined by the deduper marked as duplicates.
== Turn on Verbose Mode (<code>--verbose</code>) ==
Turn on verbose logging to get more log messages in the log and to stderr.
{{noeofBGZFParameter}}
{{paramsParameter}}
= Return Value =
Returns -1 if input parameters are invalid.
Returns the SamStatus for the reads/writes (0 on success).
