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Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments

Category Read Filters


Filter out reads that:
  • Fail platform/vendor quality checks (0x200)
  • Are unmapped (0x4)
  • Represent secondary/supplementary alignments (0x100 or 0x800)

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