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Keep only reads containing good CIGAR string

Category Read Filters


Keep only reads containing good CIGAR strings.

Good CIGAR strings have the following properties:

  • Valid according to the SAM specifications.
  • Does not start or end with deletions (with or without preceding clips).
  • Does not have consecutive deletion/insertion operators.

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