Keep only reads containing good CIGAR string
Category Read Filters
OverviewKeep 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.
GATK version 18.104.22.168-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.