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BamUtil: polishBam

48 bytes removed, 13:47, 3 April 2012
Update polish bam
== Polish BAM =Overview of the <code>polishBam</code> function of <code>bamUtil</code> =The <code>polishBam</code> program is released as part of option on the StatGen Library [[bamUtil]] executable adds/updates header lines & Tools downloadadds the RG tag to each record.
= Usage = ./bam polishBam (options) --in <codeinBamFile>polishBam--out </codeoutBamFile> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
 === Parameters ===
<pre>
Required parameters:
--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option
</pre>
 
=== Usage ===
polishBAM (options) --in <inBamFile> --out <outBamFile>
=== Return Value ===
Returns 0.
=== Example ===
Command:
<pre>
../../bin/bam polishBam --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none"
</pre>

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