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) |