Changes

== Polish BAM ==

= Overview of the <code>polishBam</code> function of <code>bamUtil</code> =

The <code>polishBam</code> program is released as part of the StatGen Library & Tools download.

The <code>polishBam</code> option on the [[bamUtil]] executable adds/updates header lines & adds the RG tag to each record.

<code>polishBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.

./bam polishBam (options) --in <inBamFile> --out <outBamFile>

 

= Parameters =

=== Parameters ===

<pre>

<pre>

   Required parameters:  

   Required parameters:  

         --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option

         --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option

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=== Return Value ===

= Return Value =

Returns 0.

Returns 0.

=== Example ===

= Example =

Command:

Command:

<pre>

<pre>

../../bin/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"

./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>

</pre>