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CleanSam (version 3.1.1.0)
If empty, upload or import a SAM/BAM dataset
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

Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:

  1. to soft-clip an alignment that hangs off the end of its reference sequence.
  2. to set MAPQ to 0 if a read is unmapped.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Additional information

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