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BamUtil: revert

1,454 bytes added, 13:07, 6 January 2014
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Additional parameters allow for the removal of any other tags in order to cleanup the SAM/BAM file.
 
NOTE: Does not reorder the BAM file after modifying the position, so the resulting file may not be sorted by coordinate.
 
= Usage =
./bam revert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cigar] [--qual] [--keepTags] [--rmBQ] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]
= Parameters =
--params : print the parameter settings
</pre>
{{PhoneHomeParamDesc}}
 
== Required Parameters==
{{InBAMInputFile}}
{{OutBAMOutputFile}}
 
==Optional Parameters==
=== Revert the CIGAR & Position (<code>--cigar</code>) ===
Update the cigar and the base position of reads to the values in the OC (cigar) & OP (base position) tags.
 
By default, the OC & OP tags are removed. Use [[Keep Tags Used for Reverting (<code>--keepTags</code>)|<code>--keepTags</code>]] to keep the OC & OP tags.
=== Revert the Quality (<code>--qual</code>) ===
Update the quality of reads to the value in the OQ tag.
= Usage =By default, the OQ tag is removed. .Use [[Keep Tags Used for Reverting (<code>--keepTags</bam revert code>)|<code>--in keepTags</code>]] to keep the OQ tag. === Keep Tags Used for Reverting (<inputFilecode> --out keepTags<outputFile/code>) ===Keep the tags that are used for reverting.sam/bam/ubam The default (ubam no option) is uncompressed bam)to remove the tags after they are used. === Remove BQ Tag (<code> [--cigar] [rmBQ</code>) ===Use the <code>--qual] [rmBQ</code> option to remove the BQ Tag. === Remove Tags (<code>--keepTags] [--rmBQ] [rmTags</code>) ===Use <code>--rmTags </code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>Tag:Type"</code> For multiple tags: <code>Tag:Type;Tag:Type[;Tag:Type]*</code>] [--noeof] [--params]... {{noeofBGZFParameter}}{{paramsParameter}} {{PhoneHomeParameters}}
= Return Value =
Returns the SamStatus for the reads/writes(0 for success, non-0 for failure).
= Example Output =

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