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BamUtil: recab (view source)

Revision as of 11:02, 15 June 2012

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=== Covariates Notes ===
 
=== Covariates Notes ===
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Duplicates are determined by checking for matching keys. 
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The Key is comprised of:
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# Chromosome
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# Orientation (forward/reverse)
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# Unclipped Start(forward)/End(reverse)
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# Library
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Rules:
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* Skip Unmapped Reads, they are not marked as duplicate
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* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:
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*# 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-
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*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record)
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* Mark both Paired-End Reads Duplicate if:
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# Another paired-end pair has the same set of keys and has a higher base quality sum.
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This code assumes that at most 1000 bases are clipped at the start of a read.
      
== How to use it ==
 
== How to use it ==
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When <code>dedup</code> is invoked without any arguments the usage information is displayed as described below under [[#Usage|Usage]].
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When <code>recab</code> is invoked without any arguments the usage information is displayed as described below under [[#Usage|Usage]].
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The input SAM/BAM file is required, [[#input File (--in)|input File (--in)]], and must be sorted by coordinate.
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The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
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The input SAM/BAM file ([[#input File (--in)|--in]]), the output SAM/BAM file ([[#output File (--out)|--out]]), and the reference file ([[#Reference File (--refFile)|--refFile]]) are required inputs.
    
= Usage =
 
= Usage =
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{{inBAMInputFile}}
 
{{inBAMInputFile}}
 
{{outBAMOutputFile}}
 
{{outBAMOutputFile}}
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== BAM File Is Sorted By Read Name (<code>--minRecabQual</code>) ==
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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 log & Summary Statistics FileName (<code>--log</code>) ==
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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.
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== Treat Reads with Mates On Different Chromosomes As Single-Ended (<code>--oneChrom</code>) ==
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== Turn on Verbose Mode (<code>--verbose</code>) ==
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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.
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Turn on verbose logging to get more log messages in the log and to stderr.
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== Recalibrate (<code>--recab</code>) ==
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{{noeofBGZFParameter}}
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{{paramsParameter}}
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This option will recalibrate the input file in addition to deduping.
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== Reference File (<code>--refFile</code>) ==
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== Remove Duplicates (<code>--rmDups</code>) ==
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The reference file to use for comparing read bases to the reference.
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Instead of marking a read as duplicate in the flag, the <code>--rmDups</code> option will remove it from the output BAM file. 
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== DBSNP File (<code>--dbsnp</code>) ==
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== Ignore Previous Duplicate Marking (<code>--force</code>) ==
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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.
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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.
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== Blended Model Weight (<code>--blended</code>) ==
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== Turn on Verbose Mode (<code>--verbose</code>) ==
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<span style="color:red">TBD - this parameter is not yet implemented.</span>
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Turn on verbose logging to get more log messages in the log and to stderr.
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== BAM File Is Sorted By Read Name (<code>--minRecabQual</code>) ==
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{{noeofBGZFParameter}}
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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 - this parameter is not yet implemented.</span>.
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{{paramsParameter}}
      
= Return Value =
 
= Return Value =
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/4957"

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