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Filter out unmapped reads

Category Read Filters


Filter out unmapped reads.

Unmapped reads are defined by three criteria:

  • SAM flag value 0x4
  • An asterisk for reference name or RNAME (column 3 of a SAM record)
  • A zero value for leftmost mapping position for POS (column 4 of SAM record)

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GATK version built at Wed, 9 Oct 2019 15:19:59 -0400.