CIGAR strings

The ‘CIGAR’ (Compact Idiosyncratic Gapped Alignment Report) string is how the SAM/BAM format represents spliced alignments.

CIGAR strings have a number of operators:

• $M$ - Match - Exact match of x positions
• $N$ - Alignment gap - Next x positions on ref don’t match
• $D$ - Deletion - Next x positions on ref don’t match
• $I$ - Insertion - Next x positions on query don’t match

Example:

CIGAR=3M2I3M:

0123456789
AAGTC  TAGAA (ref) 
  GTCGATAG (query)