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RevertOriginalBaseQualitiesAndAddMateCigar (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset

Restore original qualities from the OQ field to the QUAL field if available:

RESTORE_ORIGINAL_QUALITIES; default=True

The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset:

MAX_RECORDS_TO_EXAMINE; default=10,000

Select validation stringency:

Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

Purpose

Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Inputs, outputs, and parameters

Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.

From Picard documentation( http://broadinstitute.github.io/picard/):

RESTORE_ORIGINAL_QUALITIES=Boolean
OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.
                              Default value: true. Possible values: {true, false}

MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not
                              output, given that there are a no original base qualities (if we are to restore) and mate
                              cigars exist. Set to 0 to never skip the file.  Default value: 10000.

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .