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 220.127.116.11 built at 25-51-2019 10:51:39.