Keep only reads containing good CIGAR string
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 22.214.171.124 built at Wed, 30 Jan 2019 10:21:04 +0530.