Table 1 CIGAR operations used in GATK HC
From: GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller
| Operation | Description |
|---|---|
| M | Match/mismatch |
| I | Insertion (gap in R1) |
| D | Deletion (gap in R2) |
| S | Soft clipping (base at the beginning or the end of R2 but not in R1) |
